chr3-158732382-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_206963.2(RARRES1):c.34T>A(p.Trp12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0036 in 1,501,498 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_206963.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RARRES1 | NM_206963.2 | c.34T>A | p.Trp12Arg | missense_variant | 1/6 | ENST00000237696.10 | |
LOC100287290 | NR_171782.1 | n.22A>T | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RARRES1 | ENST00000237696.10 | c.34T>A | p.Trp12Arg | missense_variant | 1/6 | 1 | NM_206963.2 | P1 | |
ENST00000465477.5 | n.56A>T | non_coding_transcript_exon_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00269 AC: 408AN: 151950Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00186 AC: 184AN: 98962Hom.: 0 AF XY: 0.00204 AC XY: 113AN XY: 55438
GnomAD4 exome AF: 0.00371 AC: 5003AN: 1349438Hom.: 16 Cov.: 41 AF XY: 0.00364 AC XY: 2421AN XY: 665468
GnomAD4 genome AF: 0.00268 AC: 408AN: 152060Hom.: 2 Cov.: 33 AF XY: 0.00250 AC XY: 186AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | 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