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_001754.4(RUNX1):c.*3345A>T

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10652909

339810 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 86fc220e-350e-4d28-97db-e97caaba1f41

Approved on: 2020-01-13

Published on: 2020-01-14

HGVS expressions

NM_001754.4:c.*3345A>T

NM_001754.4(RUNX1):c.*3345A>T

NC_000021.9:g.34788790T>A

CM000683.2:g.34788790T>A

NC_000021.8:g.36161087T>A

CM000683.1:g.36161087T>A

NC_000021.7:g.35082957T>A

NG_011402.2:g.1200922A>T

NM_001001890.2:c.*3345A>T

ENST00000300305.7:c.*3345A>T

ENST00000344691.8:c.*3345A>T

ENST00000437180.5:c.*3345A>T

Benign

BP2 BA1

BS1 BS4 BS3 BP4 BP7 PS4 PS1 PS3 PVS1 PP1 PP3 PM5 PM4 PM1 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 NM_001754.4:c.*3345A>T variant in the 3' UTR has an MAF of 0.09 (9%, 145/1560 alleles) in the East Asian subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 16 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

This variant is reported in 16 homozygotes in gnomAD v3 and 12 homozygotes in gnomAD v2.1.1 in the East Asian population.

BA1

This 3' UTR variant is reported in gnomAD v2.1.1 at a frequency of 0.093 (145/1560 alleles) and in gnomAD v3 at a frequency of 0.08 (254/3134 alleles) in the East Asian population. It meets criteria for BA1.

BS1

Meets BA1

BS4

No data currently available

BS3

No data currently available

BP4

N/A

BP7

N/A

PS4

The variant has not been reported in patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge.

PS1

N/A

PS3

No data currently available

PVS1

N/A

PP1

No data currently available

PP3

N/A

PM5

N/A

PM4

N/A

PM1

N/A

PM2

Meets BA1

PM6

No data currently available

Curation History

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