rs1059502
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001871.3(CPB1):c.622G>A(p.Asp208Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,612,786 control chromosomes in the GnomAD database, including 44,685 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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_001871.3 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 |
---|---|---|---|---|---|---|---|
CPB1 | NM_001871.3 | c.622G>A | p.Asp208Asn | missense_variant | 7/11 | ENST00000282957.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPB1 | ENST00000282957.9 | c.622G>A | p.Asp208Asn | missense_variant | 7/11 | 1 | NM_001871.3 | P1 | |
CPB1 | ENST00000491148.5 | c.622G>A | p.Asp208Asn | missense_variant | 8/12 | 5 | P1 | ||
CPB1 | ENST00000468341.1 | c.520G>A | p.Asp174Asn | missense_variant | 6/7 | 3 | |||
CPB1 | ENST00000484877.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.244 AC: 37011AN: 151944Hom.: 4624 Cov.: 32
GnomAD3 exomes AF: 0.224 AC: 56168AN: 250960Hom.: 6710 AF XY: 0.226 AC XY: 30641AN XY: 135612
GnomAD4 exome AF: 0.231 AC: 337317AN: 1460724Hom.: 40055 Cov.: 34 AF XY: 0.232 AC XY: 168553AN XY: 726678
GnomAD4 genome ? AF: 0.244 AC: 37036AN: 152062Hom.: 4630 Cov.: 32 AF XY: 0.242 AC XY: 17955AN XY: 74342
ClinVar
Submissions by phenotype
CPB1-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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