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.36G>A (p.Ser12=)

CA10014727

239048 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9ccc823a-e760-436c-a8d0-5597cbf6853d
Approved on: 2020-04-10
Published on: 2020-06-02

HGVS expressions

NM_001754.4:c.36G>A
NM_001754.4(RUNX1):c.36G>A (p.Ser12=)
NC_000021.9:g.35048864C>T
CM000683.2:g.35048864C>T
NC_000021.8:g.36421161C>T
CM000683.1:g.36421161C>T
NC_000021.7:g.35343031C>T
NG_011402.2:g.940848G>A
ENST00000300305.7:c.36G>A
ENST00000416754.1:c.36G>A
ENST00000437180.5:c.36G>A
ENST00000455571.5:c.36G>A
ENST00000475045.6:c.36G>A
ENST00000482318.5:c.36G>A
More

Likely Benign

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

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
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: -1.41 < 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 and 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: -1.41 < 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
BP2
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
PS3
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
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
Not 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
PM2
ALL:0.0046% (13/282814 alleles) - AFR:0.0040% (1) - AMR:0.0085% (3) - EAS:0.0050% (1) - SAS:0.0033% (1) - NFE:0.0054% (7) (gnomAD v2) ALL:0.003491% (5/143210 alleles) - AFR:0.004763% (2) - AMR:0.007324% (1) - NFE:0.003098% (2) (gnomAD v3)
PM6
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
BA1
ALL:0.0046% (13/282814 alleles) - AFR:0.0040% (1) - AMR:0.0085% (3) - EAS:0.0050% (1) - SAS:0.0033% (1) - NFE:0.0054% (7) (gnomAD v2) ALL:0.003491% (5/143210 alleles) - AFR:0.004763% (2) - AMR:0.007324% (1) - NFE:0.003098% (2) (gnomAD v3)
BS1
ALL:0.0046% (13/282814 alleles) - AFR:0.0040% (1) - AMR:0.0085% (3) - EAS:0.0050% (1) - SAS:0.0033% (1) - NFE:0.0054% (7) (gnomAD v2) ALL:0.003491% (5/143210 alleles) - AFR:0.004763% (2) - AMR:0.007324% (1) - NFE:0.003098% (2) (gnomAD v3)
BS4
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
Curation History
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