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]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.444C>T (p.Thr148=)

CA10014514

339877 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2a26c020-4ebb-4160-a16b-4c5b8b5b9440

HGVS expressions

NM_001754.4:c.444C>T
NM_001754.4(RUNX1):c.444C>T (p.Thr148=)
NC_000021.9:g.34880621G>A
CM000683.2:g.34880621G>A
NC_000021.8:g.36252918G>A
CM000683.1:g.36252918G>A
NC_000021.7:g.35174788G>A
NG_011402.2:g.1109091C>T
NM_001001890.2:c.363C>T
NM_001122607.1:c.363C>T
ENST00000300305.7:c.444C>T
ENST00000344691.8:c.363C>T
ENST00000358356.9:c.363C>T
ENST00000399237.6:c.408C>T
ENST00000399240.5:c.363C>T
ENST00000437180.5:c.444C>T
ENST00000455571.5:c.405C>T
ENST00000482318.5:c.*34C>T

Likely Benign

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

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:c.444C>T (p.Thr148=) variant is a synonymous variant that 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 addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -4.3832 < 0.1) (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
BP4
Synonymous 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.
BP7
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved (phyloP100way: -4.3832 <0.1).
Not Met criteria codes
PVS1
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
BP2
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
PS1
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
BA1
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
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
PM2
MAF Allele Frequency: 0.00012 < 0.00015
PM6
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
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.