rs104894669
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001728.4(BSG):c.622G>A(p.Glu208Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000497 in 1,610,862 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Affects (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
BSG
NM_001728.4 missense
NM_001728.4 missense
Scores
5
14
Clinical Significance
Conservation
PhyloP100: 1.91
Genes affected
BSG (HGNC:1116): (basigin (Ok blood group)) The protein encoded by this gene, basigin, is a plasma membrane protein that is important in spermatogenesis, embryo implantation, neural network formation, and tumor progression. Basigin is also a member of the immunoglobulin superfamily, ubiquitously expressed in various tissues. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BSG | NM_001728.4 | c.622G>A | p.Glu208Lys | missense_variant | 4/9 | ENST00000333511.9 | NP_001719.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BSG | ENST00000333511.9 | c.622G>A | p.Glu208Lys | missense_variant | 4/9 | 1 | NM_001728.4 | ENSP00000333769.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152044Hom.: 0 Cov.: 33
GnomAD3 genomes
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33
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GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248154Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134880
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GnomAD4 exome AF: 0.0000528 AC: 77AN: 1458818Hom.: 0 Cov.: 33 AF XY: 0.0000468 AC XY: 34AN XY: 725828
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74278
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ESP6500AA
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ClinVar
Significance: Affects
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BLOOD GROUP--OK Other:1
Affects, no assertion criteria provided | literature only | OMIM | Apr 01, 1997 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;.
REVEL
Benign
Sift
Benign
T;T;.;T;.
Sift4G
Benign
T;T;T;T;T
Polyphen
0.90, 0.72
.;P;.;P;.
Vest4
MVP
MPC
0.47
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at