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]
  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.924C>T (p.Ser308=)

CA16616518

415830 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8568b183-5fdb-4f4a-b47c-4a61cbaad38e
Approved on: 2020-04-10
Published on: 2020-06-02

HGVS expressions

NM_001754.4:c.924C>T
NM_001754.4(RUNX1):c.924C>T (p.Ser308=)
NC_000021.9:g.34799344G>A
CM000683.2:g.34799344G>A
NC_000021.8:g.36171641G>A
CM000683.1:g.36171641G>A
NC_000021.7:g.35093511G>A
NG_011402.2:g.1190368C>T
NM_001001890.2:c.843C>T
NM_001001890.3:c.843C>T
ENST00000300305.7:c.924C>T
ENST00000344691.8:c.843C>T
ENST00000399240.5:c.651C>T
ENST00000437180.5:c.924C>T
ENST00000482318.5:c.*514C>T
More

Likely Benign

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

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The synonymous 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; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -0.68 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7.
Met criteria codes
BP7
This synonymous 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. In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -0.68 < 0.1 [-14.1;6.4]).
BP4
This synonymous 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.
Not Met criteria codes
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
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
PM2
Absent from gnomAD v2 ALL:0.001396% (2/143284 alleles) - AMR:0.007323% (1) - AFR:0.002379% (1) (gnomAD v3)
PM6
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
Not located at a hotspot (R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R210, R204) or within residues 105-204.
PM5
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
BS1
Absent from gnomAD v2 ALL:0.001396% (2/143284 alleles) - AMR:0.007323% (1) - AFR:0.002379% (1) (gnomAD v3)
BS3
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
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Absent from gnomAD v2 ALL:0.001396% (2/143284 alleles) - AMR:0.007323% (1) - AFR:0.002379% (1) (gnomAD v3)
Curation History
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