Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001130987.2(DYSF):c.1914C>T (p.Tyr638=)

CA147728

94282 (ClinVar)

Gene: DYSF
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: bdd67f28-7d85-48f3-82de-e055885811a7
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_001130987.2:c.1914C>T
NM_001130987.2(DYSF):c.1914C>T (p.Tyr638=)
NC_000002.12:g.71553118C>T
CM000664.2:g.71553118C>T
NC_000002.11:g.71780248C>T
CM000664.1:g.71780248C>T
NC_000002.10:g.71633756C>T
NG_008694.1:g.104496C>T
ENST00000258104.8:c.1860C>T
ENST00000410020.8:c.1914C>T
ENST00000258104.7:c.1860C>T
ENST00000394120.6:c.1863C>T
ENST00000409366.5:c.1863C>T
ENST00000409582.7:c.1911C>T
ENST00000409651.5:c.1956C>T
ENST00000409744.5:c.1821C>T
ENST00000409762.5:c.1911C>T
ENST00000410020.7:c.1914C>T
ENST00000410041.1:c.1914C>T
ENST00000413539.6:c.1953C>T
ENST00000429174.6:c.1860C>T
NM_001130455.1:c.1863C>T
NM_001130976.1:c.1818C>T
NM_001130977.1:c.1818C>T
NM_001130978.1:c.1860C>T
NM_001130979.1:c.1953C>T
NM_001130980.1:c.1911C>T
NM_001130981.1:c.1911C>T
NM_001130982.1:c.1956C>T
NM_001130983.1:c.1863C>T
NM_001130984.1:c.1821C>T
NM_001130985.1:c.1914C>T
NM_001130986.1:c.1821C>T
NM_001130987.1:c.1914C>T
NM_003494.3:c.1860C>T
NM_001130455.2:c.1863C>T
NM_001130976.2:c.1818C>T
NM_001130977.2:c.1818C>T
NM_001130978.2:c.1860C>T
NM_001130979.2:c.1953C>T
NM_001130980.2:c.1911C>T
NM_001130981.2:c.1911C>T
NM_001130982.2:c.1956C>T
NM_001130983.2:c.1863C>T
NM_001130984.2:c.1821C>T
NM_001130985.2:c.1914C>T
NM_001130986.2:c.1821C>T
NM_003494.4:c.1860C>T
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 25
PS2 PS4 PS3 PS1 PVS1 PP4 PP1 PP3 PP2 PM6 PM2 PM3 PM1 PM4 PM5 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DYSF Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_003494.4: c.1860C>T (p.Tyr620=) variant in DYSF, which is also known as NM_001130987.2: c.1914C>T (p.Tyr638=), is a synonymous (silent) variant that is not located in a splice region (outside of the first and the last 3 bases of the exon). The filtering allele frequency is 0.05612 for South Asian exome chromosomes in gnomAD v2.1.1 (the lower threshold of the 95% CI of 1787/30616), which is higher than the VCEP threshold of 0.003 (BA1). The SpliceAI prediction score for this variant is 0.08, which is greater than the VCEP threshold of <0.05 (BP4 and BP7 not applied). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 1.0.0; 01/08/2025): BA1.
Met criteria codes
BA1
The filtering allele frequency (the lower threshold of the 95% CI of 1787/30616) of the c.1860C>T variant in DYSF is 0.05612 for South Asian exome chromosomes in gnomAD v2.1.1, which is higher than the ClinGen LGMD VCEP threshold (>0.003) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
The NM_003494.4: c.1860C>T (p.Tyr620=) variant is a synonymous (silent) variant that is not located in a splice region (outside of the first and the last 3 bases of the exon). It occurs at a nucleotide that is not conserved as shown by PhyloP (score -3.5 < VCEP threshold of 0.1). BP4 and BP7 were not applied because the SpliceAI prediction score of 0.08 is greater than the VCEP threshold of 0.05.
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
The NM_003494.4: c.1860C>T (p.Tyr620=) variant is a synonymous (silent) variant that is not located in a splice region (outside of the first and the last 3 bases of the exon). BP4 and BP7 were not applied because the SpliceAI prediction score of 0.08 is greater than the VCEP threshold of 0.05.
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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