Variant: NM_001754.4(RUNX1):c.614-34C>T

CA10014405

258186 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

UUID: e7c466ba-2630-4273-adcf-da7d8ca99b52

HGVS expressions

NM_001754.4:c.614-34C>T
NM_001754.4(RUNX1):c.614-34C>T
NC_000021.9:g.34834635G>A
CM000683.2:g.34834635G>A
NC_000021.8:g.36206932G>A
CM000683.1:g.36206932G>A
NC_000021.7:g.35128802G>A
NG_011402.2:g.1155077C>T
NM_001001890.2:c.533-34C>T
NM_001122607.1:c.533-34C>T
ENST00000300305.7:c.614-34C>T
ENST00000344691.8:c.533-34C>T
ENST00000358356.9:c.533-34C>T
ENST00000399237.6:c.578-34C>T
ENST00000399240.5:c.532+24839C>T
ENST00000437180.5:c.614-34C>T
ENST00000469087.1:n.150-34C>T
ENST00000482318.5:c.*204-34C>T

Benign

• Met criteria codes: BP2 BP4 BA1

• Not Met criteria codes: BS4 BS1 BS3 PVS1 BP7 PS4 PS1 PS3 PP1 PP3 PM5 PM1 PM4 PM6 PM2

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Evidence submitted by expert panel

Myeloid Malignancy VCEP

The NM_001754.4:c.614-34C>T variant has a MAF of 1 (100%) in gnomAD cohort that is ≥ 0.0015 (0.15%) (BA1). This variant is detected in homozygous state in gnomAD population database (BP2). This intronic variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4.

Met criteria codes

• BP2: This variant is detected in homozygous state in gnomAD population database.
• BP4: Intronic variant for which SSF and MES predict either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% AND no putative cryptic splice sites are created.
• BA1: gnomAD Allele Frequency: 1

Not Met criteria codes

• BS4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS3: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PVS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP7: phyloP100way: 1.06724 >0.1
• PS4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS3: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP3: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM6: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

Approved on: 2019-07-26

Published on: 2019-08-02