Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.351+1G>C

CA16616270

409822 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 5671cfda-4808-4020-8702-22f1816745bd

HGVS expressions

NM_001754.4:c.351+1G>C
NM_001754.4(RUNX1):c.351+1G>C
NC_000021.9:g.34886842C>G
CM000683.2:g.34886842C>G
NC_000021.8:g.36259139C>G
CM000683.1:g.36259139C>G
NC_000021.7:g.35181009C>G
NG_011402.2:g.1102870G>C
NM_001001890.2:c.270+1G>C
NM_001122607.1:c.270+1G>C
ENST00000300305.7:c.351+1G>C
ENST00000344691.8:c.270+1G>C
ENST00000358356.9:c.270+1G>C
ENST00000399237.6:c.315+1G>C
ENST00000399240.5:c.270+1G>C
ENST00000437180.5:c.351+1G>C
ENST00000455571.5:c.312+1G>C
ENST00000482318.5:c.59-6129G>C

Likely Pathogenic

Met criteria codes 2
PM2 PVS1
Not Met criteria codes 16
PM5 PM4 PM1 PM6 BA1 BS3 BS1 BS4 BP7 BP4 BP2 PS1 PS3 PS4 PP3 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The NM_001754.4(RUNX1):c.351+1G>C variant is a canonical splice site variant that is predicted to introduce a frameshift and a premature stop codon and expected to result in nonsense-mediated mRNA decay (PVS1). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1, PM2.
Met criteria codes
PM2
The variant is absent from all population databases.
PVS1
A variant at canonical splice site (+1). The transcription predicts to skip exon 4 and generates a frameshift (-1) that predicts to undergo NMD.
Not Met criteria codes
PM5
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
PM1
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
BA1
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
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
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
PS4
SCV000550165.2: germline status not confirmed. SCV000807778.1: insufficient data
PP3
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
Approved on: 2019-08-01
Published on: 2019-08-02
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