10-100069757-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001308.3(CPN1):c.533G>A(p.Gly178Asp) variant causes a missense change. The variant allele was found at a frequency of 0.043 in 1,613,682 control chromosomes in the GnomAD database, including 1,667 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001308.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0346 AC: 5254AN: 151744Hom.: 131 Cov.: 31
GnomAD3 exomes AF: 0.0423 AC: 10647AN: 251480Hom.: 255 AF XY: 0.0420 AC XY: 5711AN XY: 135912
GnomAD4 exome AF: 0.0438 AC: 64060AN: 1461822Hom.: 1536 Cov.: 32 AF XY: 0.0437 AC XY: 31788AN XY: 727222
GnomAD4 genome AF: 0.0346 AC: 5255AN: 151860Hom.: 131 Cov.: 31 AF XY: 0.0335 AC XY: 2483AN XY: 74202
ClinVar
Submissions by phenotype
Anaphylotoxin inactivator deficiency Pathogenic:1Benign:1
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not specified Benign:1
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 in ESP (all):461/13006=3.54% -
not provided Benign:1
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CPN1-related disorder Benign:1
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