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.*2201dup

CA10650422

339837 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 99a689b0-3c05-4d64-9af3-b0a1da2540b5

Approved on: 2020-05-13

Published on: 2020-06-02

HGVS expressions

NM_001754.4:c.*2201dup

NM_001754.4:c.*2201dupT

NM_001754.4(RUNX1):c.*2201dup

NC_000021.9:g.34789941dup

CM000683.2:g.34789941dup

NC_000021.8:g.36162238dup

CM000683.1:g.36162238dup

NC_000021.7:g.35084108dup

NG_011402.2:g.1199778dup

NM_001001890.2:c.*2201dup

NM_001001890.3:c.*2201dup

ENST00000300305.7:c.*2201dup

ENST00000344691.8:c.*2201dup

ENST00000437180.5:c.*2201dup

Benign

BA1 BP2

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

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 RUNX1 c.*2201dup variant in the 3' UTR has an MAF of 0.02216 (2.2%, 1429/64490 alleles) in the non-Finnish European subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 26 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.

BA1

The c.*2201dup variant is reported at the highest MAF in the non-Finnish European population in gnomAD v3, at a frequency of 0.02216 (1429/64490 alleles), with 19 homozygotes.

BP2

A total of 6 and 26 homozygotes are reported in gnomAD v2.1.1 and v3 , respectively.

PVS1

N/A

BP7

N/A

BP4

N/A

BS1

Variant meets BA1

BS3

N/A

BS4

N/A

PP3

N/A

PP1

N/A

PS3

N/A

PS4

Variant meets BA1

PS1

N/A

PM4

N/A

PM1

N/A

PM5

N/A

PM2

Variant meets BA1

PM6

N/A

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