chr2-203440009-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_213589.3(RAPH1):c.3181G>A(p.Val1061Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,402 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_213589.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPH1 | NM_213589.3 | c.3181G>A | p.Val1061Met | missense_variant | 14/14 | ENST00000319170.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPH1 | ENST00000319170.10 | c.3181G>A | p.Val1061Met | missense_variant | 14/14 | 1 | NM_213589.3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151822Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250746Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135648
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461580Hom.: 1 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 727066
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151822Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74134
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at