chr5-178994769-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000843.4(GRM6):āc.176A>Cā(p.Gln59Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 1,369,858 control chromosomes in the GnomAD database, including 240,162 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q59Q) has been classified as Likely benign.
Frequency
Consequence
NM_000843.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM6 | NM_000843.4 | c.176A>C | p.Gln59Pro | missense_variant | 2/11 | ENST00000517717.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM6 | ENST00000517717.3 | c.176A>C | p.Gln59Pro | missense_variant | 2/11 | 5 | NM_000843.4 | P1 | |
GRM6 | ENST00000231188.9 | c.176A>C | p.Gln59Pro | missense_variant | 1/10 | 2 | P1 | ||
GRM6 | ENST00000650031.1 | c.176A>C | p.Gln59Pro | missense_variant | 3/12 | P1 |
Frequencies
GnomAD3 genomes AF: 0.571 AC: 85484AN: 149760Hom.: 24568 Cov.: 34
GnomAD3 exomes AF: 0.550 AC: 37270AN: 67784Hom.: 10477 AF XY: 0.539 AC XY: 21289AN XY: 39532
GnomAD4 exome AF: 0.591 AC: 720965AN: 1219992Hom.: 215565 Cov.: 41 AF XY: 0.586 AC XY: 351108AN XY: 599334
GnomAD4 genome AF: 0.571 AC: 85561AN: 149866Hom.: 24597 Cov.: 34 AF XY: 0.572 AC XY: 41803AN XY: 73122
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 16, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2Other:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided, no classification provided | literature only | Retina International | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Congenital stationary night blindness 1B Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at