16-19536425-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001323572.2(CCP110):āc.756C>Gā(p.Ile252Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 1,613,540 control chromosomes in the GnomAD database, including 651,781 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 ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001323572.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCP110 | NM_001323572.2 | c.756C>G | p.Ile252Met | missense_variant | 4/14 | ENST00000694978.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCP110 | ENST00000694978.1 | c.756C>G | p.Ile252Met | missense_variant | 4/14 | NM_001323572.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.908 AC: 138114AN: 152170Hom.: 62942 Cov.: 32
GnomAD3 exomes AF: 0.869 AC: 217675AN: 250590Hom.: 95625 AF XY: 0.861 AC XY: 116634AN XY: 135540
GnomAD4 exome AF: 0.895 AC: 1308305AN: 1461252Hom.: 588787 Cov.: 41 AF XY: 0.889 AC XY: 646020AN XY: 726922
GnomAD4 genome AF: 0.908 AC: 138222AN: 152288Hom.: 62994 Cov.: 32 AF XY: 0.903 AC XY: 67247AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at