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_001754.5(RUNX1):c.*3297T>C

Curation Version - 1.1
Curation History
JSON LD for Version 1.1

CA10650415

339811 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 860c5d4e-cb6a-4d95-baf9-403cdc0aa381

Approved on: 2024-09-11

Published on: 2024-09-11

HGVS expressions

NM_001754.5:c.*3297T>C

NM_001754.5(RUNX1):c.*3297T>C

NC_000021.9:g.34788838A>G

CM000683.2:g.34788838A>G

NC_000021.8:g.36161135A>G

CM000683.1:g.36161135A>G

NC_000021.7:g.35083005A>G

NG_011402.2:g.1200874T>C

ENST00000675419.1:c.*3297T>C

ENST00000300305.7:c.*3297T>C

ENST00000344691.8:c.*3297T>C

ENST00000437180.5:c.*3297T>C

NM_001001890.2:c.*3297T>C

NM_001754.4:c.*3297T>C

NM_001001890.3:c.*3297T>C

Uncertain Significance

PVS1 BA1 BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM6 PM2 PM1 PM3 PM4 PM5

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Criteria Specification: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.*3297T>C is a UTR variant which does not meet any ACMG/AMP criteria. In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: None.

PVS1

This variant is not a null variant, not impacting any of the following processes or sites: Nonsense, frameshift, canonical +/- 1 or 2 splice sites, initiation codon, single exon deletion, multiple exon deletions

BA1

Variant is not present in population databases (gnomAD v2.1 or v3.1.2) at a high enough threshhold. Found in gnomAD v2, East Asian Population at 0.064% (1/1560, 0.00064). Variant is present in less than 5 alleles, in a population set of less than 2000, so does not qualify to be evaluated by population codes.

BS2

This variant has not been reported in probands

BS4

This variant has not been reported in probands in literature.

BS3

This variant has not been featured in in vitro or in vivo functional studies that show no damaging effect on protein function or splicing.

BS1

BP5

This rule is not applicable for MM-VCEP

BP7

UTR variant

BP2

This variant has not been detected in a homozygous state in an individual or in a population database (gnomAD). This variant has not been observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

BP3

This is not an in frame deletion insertion.

BP4

This 3'UTR variant does not have a SpliceAI score of ≥ 0.38, as SpliceAI is unable to return results at this cDNA location.

BP1

This rule is not applicable for MM-VCEP

PS2

This variant has not been reported in probands in the literature.

PS4

This variant has not been reported in probands

PS3

This variant has not been featured in in vitro or in vivo functional studies showing a damaging effect on the gene or gene product.

PS1

This is not a missense variant, and there has not yet been a missense change determined to be pathogenic at this amino acid residue.

PP4

This rule is not applicable for MM-VCEP

PP1

This variant was not found to co-segregate with disease in multiple affected family members.

PP3

This 3'UTR variant does not have a SpliceAI score of ≥ 0.38, as SpliceAI is unable to return results at this cDNA location.

PP2

This rule is not applicable for MM-VCEP

PM6

This variant has not been reported in probands in the literature.

PM2

Variant is present in gnomAD v2, East Asian Population at 0.064% (1/1560, 0.00064). Variant is present in less than 5 alleles, in a population set of less than 2000, so does not qualify to be evaluated by population codes.

PM1

This variant does not affect any of the following amino acid residues, nor is it located within the RHD: R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204 NOR is it within residues 89-204

PM3

This rule is not applicable for MM-VCEP

PM4

This is not an in frame deletion insertion.

PM5

This is not a missense variant, and there has not yet been a different missense change determined to be pathogenic at this amino acid residue.

Curation History

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