rs6131
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003005.4(SELP):c.992G>A(p.Ser331Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,613,720 control chromosomes in the GnomAD database, including 30,311 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003005.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELP | NM_003005.4 | c.992G>A | p.Ser331Asn | missense_variant | 7/17 | ENST00000263686.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELP | ENST00000263686.11 | c.992G>A | p.Ser331Asn | missense_variant | 7/17 | 1 | NM_003005.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.222 AC: 33723AN: 151900Hom.: 4136 Cov.: 32
GnomAD3 exomes AF: 0.198 AC: 49569AN: 250832Hom.: 5435 AF XY: 0.201 AC XY: 27189AN XY: 135526
GnomAD4 exome AF: 0.184 AC: 268245AN: 1461702Hom.: 26158 Cov.: 35 AF XY: 0.186 AC XY: 135318AN XY: 727152
GnomAD4 genome ? AF: 0.222 AC: 33769AN: 152018Hom.: 4153 Cov.: 32 AF XY: 0.220 AC XY: 16330AN XY: 74324
ClinVar
Submissions by phenotype
SELP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at