13-46073959-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001872.5(CPB2):c.505G>A(p.Ala169Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,578,308 control chromosomes in the GnomAD database, including 83,515 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_001872.5 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 |
---|---|---|---|---|---|---|---|
CPB2 | NM_001872.5 | c.505G>A | p.Ala169Thr | missense_variant | 6/11 | ENST00000181383.10 | |
CPB2-AS1 | NR_046226.1 | n.119-20894C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPB2 | ENST00000181383.10 | c.505G>A | p.Ala169Thr | missense_variant | 6/11 | 1 | NM_001872.5 | P1 | |
CPB2-AS1 | ENST00000663159.1 | n.469+20994C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.343 AC: 51867AN: 151216Hom.: 9105 Cov.: 30
GnomAD3 exomes AF: 0.312 AC: 78096AN: 250340Hom.: 12551 AF XY: 0.308 AC XY: 41595AN XY: 135262
GnomAD4 exome AF: 0.319 AC: 455760AN: 1426978Hom.: 74404 Cov.: 31 AF XY: 0.316 AC XY: 223469AN XY: 706124
GnomAD4 genome ? AF: 0.343 AC: 51903AN: 151330Hom.: 9111 Cov.: 30 AF XY: 0.343 AC XY: 25377AN XY: 73894
ClinVar
Submissions by phenotype
CPB2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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