rs1249153560
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002401.5(MAP3K3):c.937C>T(p.Arg313Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250574Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135540
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727124
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Cerebral cavernous malformations 5 Uncertain:1
A MAP3K3 c.937C>T (p.Arg313Cys) variant was identified at a near heterozygous allelic fraction of 47.3%, a frequency that may be consistent with germline origin. To our knowledge, it has not been reported in the medical literature. The MAP3K3 c.937C>T (p.Arg313Cys) variant is only observed on 19/1,613,884 alleles in the general population (gnomAD v.4.1.0), indicating it is not a common variant. Computational predictors are uncertain as to the impact of this variant on MAP3K3 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of MAP3K3 c.937C>T (p.Arg313Cys) variant is uncertain at this time. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at