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.84T>C (p.Ser28=)

CA512319034

1156194 (ClinVar)

Gene: RUNX1 (HGNC:861)

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome (MONDO:0011071)

Inheritance Mode: Autosomal dominant inheritance

UUID: 74b8c298-a7d1-4620-bc17-21b748ea7800

Approved on: 2026-05-04

Published on: 2026-05-04

HGVS expressions

NM_001754.5(RUNX1):c.84T>C (p.Ser28=)

NM_001754.5:c.84T>C

NC_000021.9:g.34892938A>G

CM000683.2:g.34892938A>G

NC_000021.8:g.36265235A>G

CM000683.1:g.36265235A>G

NC_000021.7:g.35187105A>G

NG_011402.2:g.1096774T>C

ENST00000675419.1:c.84T>C

ENST00000300305.7:c.84T>C

ENST00000416754.1:c.84T>C

ENST00000437180.5:c.84T>C

ENST00000455571.5:c.59-5842T>C

ENST00000475045.6:c.84T>C

ENST00000482318.5:c.59-12225T>C

NM_001754.4:c.84T>C

Likely Benign

BP7 BP4 PM2_Supporting

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

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 for RUNX1 Version 3.1.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.84T>C is a synonymous variant which has a SpliceAI score ≤ 0.20 (0.11) (BP4, BP7). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7, PM2_supporting.

BP7

The SpliceAI score is <0.2

BP4

This is a synonymous variant that is not predicted to impact splicing. (SpliceAI < 0.2)

PM2_Supporting

This variant is completely absent from gnomAD with at least 20x coverage for RUNX1 (PM2_supporting).

BS2

This rule is not applicable for MM-VCEP

PVS1

This is a synonymous variant.

BS4

There are no published case studies as of 24/01/2023 that have included this variant.

BS3

There is no literature as of 24/01/2023 that have studied this variant.

BS1

Allele is absent from ExAC, 1000Genomes and ESP.

BP5

This rule is not applicable for MM-VCEP

BP1

This rule is not applicable for MM-VCEP.

BP2

There are no published studies as of 24/01/2023 that have included this variant.

BP3

This rule is not applicable for MM-VCEP

PS1

This is a synonymous variant.

PS4

As of 24/02/2023 there are no reports of this variant in the literature.

PS2

There are no published case studies as of 24/01/2023 that have included this variant.

PS3

There is no literature as of 24/01/2023 that have studied this variant.

BA1

Allele is absent from ExAC, 1000Genomes and ESP.

PP3

This synonymous variant is not predicted to impact splicing.

PP2

This rule is not applicable for MM-VCEP.

PP1

There are no published case studies as of 24/01/2023 that have included this variant.

PP4

This rule is not applicable for MM-VCEP

PM6

There are no published case studies as of 24/01/2023 that have included this variant.

PM5

This is a synonymous variant.

PM1

This variant is not within one of the established hot spots.

PM3

This rule is not applicable for MM-VCEP

PM4

Variant is a synonymous variant not resulting in in-frame del/insertions or stop-loss.

Curation History

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