rs1926447
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001872.5(CPB2):āc.1040T>Cā(p.Ile347Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,595,210 control chromosomes in the GnomAD database, including 421,043 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 (ā ). 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.1040T>C | p.Ile347Thr | missense_variant | 10/11 | ENST00000181383.10 | |
CPB2-AS1 | NR_046226.1 | n.118+2844A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPB2 | ENST00000181383.10 | c.1040T>C | p.Ile347Thr | missense_variant | 10/11 | 1 | NM_001872.5 | P1 | |
CPB2-AS1 | ENST00000663159.1 | n.469+2844A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.764 AC: 116212AN: 152012Hom.: 44878 Cov.: 32
GnomAD3 exomes AF: 0.740 AC: 182894AN: 247026Hom.: 68323 AF XY: 0.731 AC XY: 97791AN XY: 133694
GnomAD4 exome AF: 0.720 AC: 1038535AN: 1443080Hom.: 376117 Cov.: 28 AF XY: 0.718 AC XY: 515617AN XY: 718496
GnomAD4 genome ? AF: 0.765 AC: 116316AN: 152130Hom.: 44926 Cov.: 32 AF XY: 0.769 AC XY: 57150AN XY: 74354
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