Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001130987.2(DYSF):c.3898-4C>G

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA1706771

291062 (ClinVar)

Gene: DYSF

Condition: autosomal recessive limb-girdle muscular dystrophy

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: e1bf71aa-dc38-41c5-8871-6741d7bddf84

Approved on: 2025-01-09

Published on: 2025-01-09

HGVS expressions

NM_001130987.2:c.3898-4C>G

NM_001130987.2(DYSF):c.3898-4C>G

NC_000002.12:g.71601495C>G

CM000664.2:g.71601495C>G

NC_000002.11:g.71828625C>G

CM000664.1:g.71828625C>G

NC_000002.10:g.71682133C>G

NG_008694.1:g.152873C>G

ENST00000698057.1:c.1270-4C>G

ENST00000698058.1:c.487-4C>G

ENST00000698059.1:c.487-4C>G

ENST00000258104.8:c.3844-4C>G

ENST00000410020.8:c.3898-4C>G

ENST00000258104.7:c.3844-4C>G

ENST00000394120.6:c.3847-4C>G

ENST00000409366.5:c.3847-4C>G

ENST00000409582.7:c.3895-4C>G

ENST00000409651.5:c.3940-4C>G

ENST00000409744.5:c.3805-4C>G

ENST00000409762.5:c.3895-4C>G

ENST00000410020.7:c.3898-4C>G

ENST00000410041.1:c.3898-4C>G

ENST00000413539.6:c.3937-4C>G

ENST00000429174.6:c.3844-4C>G

ENST00000472873.5:n.224C>G

ENST00000479049.6:n.729-4C>G

ENST00000494501.5:n.200C>G

NM_001130455.1:c.3847-4C>G

NM_001130976.1:c.3802-4C>G

NM_001130977.1:c.3802-4C>G

NM_001130978.1:c.3844-4C>G

NM_001130979.1:c.3937-4C>G

NM_001130980.1:c.3895-4C>G

NM_001130981.1:c.3895-4C>G

NM_001130982.1:c.3940-4C>G

NM_001130983.1:c.3847-4C>G

NM_001130984.1:c.3805-4C>G

NM_001130985.1:c.3898-4C>G

NM_001130986.1:c.3805-4C>G

NM_001130987.1:c.3898-4C>G

NM_003494.3:c.3844-4C>G

NM_001130455.2:c.3847-4C>G

NM_001130976.2:c.3802-4C>G

NM_001130977.2:c.3802-4C>G

NM_001130978.2:c.3844-4C>G

NM_001130979.2:c.3937-4C>G

NM_001130980.2:c.3895-4C>G

NM_001130981.2:c.3895-4C>G

NM_001130982.2:c.3940-4C>G

NM_001130983.2:c.3847-4C>G

NM_001130984.2:c.3805-4C>G

NM_001130985.2:c.3898-4C>G

NM_001130986.2:c.3805-4C>G

NM_003494.4:c.3844-4C>G

Likely Benign

BS1 BP4

BP7 PM3

Evidence Links 0

Expert Panel

Limb Girdle Muscular Dystrophy VCEP

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.38844-4C>G variant in DYSF, which is also known as NM_001130987.2: c.3898-4C>G, is an intronic variant located in intron 34 of 54. The filtering allele frequency for this variant is 0.001881 for the South Asian population in gnomAD v4.1.0 (the lower threshold of the 95% CI of 184/86258 exome chromosomes), which is greater than the ClinGen LGMD VCEP threshold of 0.001 for BS1, and therefore meets this criterion (BS1). While this variant is located in a splice region (+7/-21) (BP7 not met), the SpliceAI score is 0.03, which is less than the LGMD VCEP threshold of 0.05 (BP4). This variant appears to have been reported in an individual undergoing genetic testing for muscular dystrophy, but only as a single hit (LOVD DYSF_001370). In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the LGMD VCEP (LGMD VCEP specifications version 1.0.0; 01/09/2025): BS1, BP4.

BS1

The filtering allele frequency for this variant is 0.001881 for the South Asian population in gnomAD v4.1.0 (the lower threshold of the 95% CI of 184/86258 exome chromosomes), which is greater than the ClinGen LGMD VCEP threshold of 0.001 for BS1, and therefore meets this criterion (BS1).

BP4

The SpliceAI score for this variant is 0.03, which is less than the LGMD VCEP threshold of 0.05 (BP4).

BP7

This variant is located in a splice region (+7/-21) (BP7 not met).

PM3

Only reported as a single hit (LOVD DYSF_001370).

Curation History

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