rs2067011
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000843.4(GRM6):āc.1353T>Cā(p.Asn451Asn) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 1,609,530 control chromosomes in the GnomAD database, including 239,795 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000843.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRM6 | NM_000843.4 | c.1353T>C | p.Asn451Asn | splice_region_variant, synonymous_variant | 7/11 | ENST00000517717.3 | NP_000834.2 | |
ZNF454 | XR_007058600.1 | n.5644-811A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRM6 | ENST00000517717.3 | c.1353T>C | p.Asn451Asn | splice_region_variant, synonymous_variant | 7/11 | 5 | NM_000843.4 | ENSP00000430767.1 |
Frequencies
GnomAD3 genomes AF: 0.507 AC: 76999AN: 151864Hom.: 19925 Cov.: 32
GnomAD3 exomes AF: 0.532 AC: 130866AN: 246060Hom.: 35216 AF XY: 0.526 AC XY: 70212AN XY: 133386
GnomAD4 exome AF: 0.547 AC: 797723AN: 1457548Hom.: 219841 Cov.: 35 AF XY: 0.543 AC XY: 393665AN XY: 725056
GnomAD4 genome AF: 0.507 AC: 77071AN: 151982Hom.: 19954 Cov.: 32 AF XY: 0.509 AC XY: 37825AN XY: 74278
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 23, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2Other:1
not provided, no classification provided | literature only | Retina International | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
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