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]
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  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.1440C>T (p.Tyr480=)

CA512232098

463985 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 635e63cd-3200-442c-88d6-aad38cbcd7b5
Approved on: 2021-01-12
Published on: 2021-01-12

HGVS expressions

NM_001754.4:c.1440C>T
NM_001754.4(RUNX1):c.1440C>T (p.Tyr480=)
NM_001001890.2:c.1359C>T
NM_001001890.3:c.1359C>T
NM_001754.5:c.1440C>T
ENST00000300305.7:c.1440C>T
ENST00000344691.8:c.1359C>T
ENST00000399240.5:c.1167C>T
ENST00000437180.5:c.1440C>T
ENST00000482318.5:c.*1030C>T
NC_000021.9:g.34792138G>A
CM000683.2:g.34792138G>A
NC_000021.8:g.36164435G>A
CM000683.1:g.36164435G>A
NC_000021.7:g.35086305G>A
NG_011402.2:g.1197574C>T

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 16
BS1 BS3 BS4 BP2 PVS1 PS1 PS3 PS4 BA1 PP3 PP1 PM4 PM1 PM5 PM2 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score = 0.223181 in GRCh37/0.744953 in GRCh38 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7.
Met criteria codes
BP7
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score = 0.223181 in GRCh37/0.744953 in GRCh38).
BP4
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score, and no putative cryptic splice sites are created.
Not Met criteria codes
BS1
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.0007012% (1/142616 alleles) - NFE:0.001554% (1/64346 alleles, no homozygotes)
BS3
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
BP2
No homozygotes in gnomAD. No case reports.
PVS1
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
PS3
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
BA1
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.0007012% (1/142616 alleles) - NFE:0.001554% (1/64346 alleles, no homozygotes)
PP3
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score, and no putative cryptic splice sites are created.
PP1
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
PM1
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
PM2
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.0007012% (1/142616 alleles) - NFE:0.001554% (1/64346 alleles, no homozygotes)
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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