1-168085631-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001375883.1(GPR161):c.1490G>A(p.Gly497Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00053 in 1,613,822 control chromosomes in the GnomAD database, including 6 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 (★). Synonymous variant affecting the same amino acid position (i.e. G497G) has been classified as Likely benign.
Frequency
Consequence
NM_001375883.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR161 | NM_001375883.1 | c.1490G>A | p.Gly497Asp | missense_variant | Exon 6 of 6 | ENST00000682931.1 | NP_001362812.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000738 AC: 185AN: 250796Hom.: 0 AF XY: 0.000825 AC XY: 112AN XY: 135746
GnomAD4 exome AF: 0.000545 AC: 796AN: 1461534Hom.: 6 Cov.: 32 AF XY: 0.000611 AC XY: 444AN XY: 727080
GnomAD4 genome AF: 0.000394 AC: 60AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74466
ClinVar
Submissions by phenotype
GPR161-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at