rs115098969
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006642.5(SDCCAG8):c.1094G>A(p.Arg365Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,614,050 control chromosomes in the GnomAD database, including 4 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R365T) has been classified as Likely benign.
Frequency
Consequence
NM_006642.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDCCAG8 | NM_006642.5 | c.1094G>A | p.Arg365Lys | missense_variant | Exon 10 of 18 | ENST00000366541.8 | NP_006633.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDCCAG8 | ENST00000366541.8 | c.1094G>A | p.Arg365Lys | missense_variant | Exon 10 of 18 | 1 | NM_006642.5 | ENSP00000355499.3 | ||
SDCCAG8 | ENST00000435549.1 | c.434G>A | p.Arg145Lys | missense_variant | Exon 5 of 11 | 1 | ENSP00000410200.1 |
Frequencies
GnomAD3 genomes AF: 0.00206 AC: 314AN: 152086Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000525 AC: 132AN: 251400Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135872
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461846Hom.: 3 Cov.: 31 AF XY: 0.000129 AC XY: 94AN XY: 727216
GnomAD4 genome AF: 0.00208 AC: 316AN: 152204Hom.: 1 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:5
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not specified Benign:2
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SDCCAG8-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Inborn genetic diseases Benign:1
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. -
Senior-Loken syndrome 7;C3889474:Bardet-Biedl syndrome 16 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at