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]

Link to SEPIO compliant JSON-LD document

Variant: NM_001754.4(RUNX1):c.*3619A>G

CA10652906

339802 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: a3156b5a-f778-4a4a-9a67-d1364c25bb90

Approved on: 2020-05-13

Published on: 2020-06-02

HGVS expressions

NM_001754.4:c.*3619A>G

NM_001754.4(RUNX1):c.*3619A>G

NC_000021.9:g.34788516T>C

CM000683.2:g.34788516T>C

NC_000021.8:g.36160813T>C

CM000683.1:g.36160813T>C

NC_000021.7:g.35082683T>C

NG_011402.2:g.1201196A>G

NM_001001890.2:c.*3619A>G

NM_001001890.3:c.*3619A>G

ENST00000300305.7:c.*3619A>G

ENST00000344691.8:c.*3619A>G

ENST00000437180.5:c.*3619A>G

Benign

BP2 BA1

PM2 PM6 PM5 PM4 PM1 BS1 BS3 BS4 BP4 BP7 PVS1 PS1 PS3 PS4 PP3 PP1

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

The c.*3619A>G variant in the 3' UTR has an MAF of 0.02813 (2.8%, 384/13650 alleles) in the Latino subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 11 individuals in the gnomAD v3 population database (BP2). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2.

BP2

A total of 11 homozygous individuals reported in gnomAD v3.

BA1

The c.*3619A>G variant is reported at the highest MAF in the Latino population in gnomAD v3, at a frequency of 0.02813 (384/13650 alleles), with 6 homozygotes.

PM2

Variant meets BA1

PM6

N/A

PM5

N/A

PM4

N/A

PM1

N/A

BS1

Variant meets BA1

BS3

N/A

BS4

N/A

BP4

N/A

BP7

N/A

PVS1

N/A

PS1

N/A

PS3

N/A

PS4

Variant meets BA1

PP3

N/A

PP1

N/A

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