rs143711180
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_014679.5(CEP57):c.677G>A(p.Arg226His) variant causes a missense change. The variant allele was found at a frequency of 0.000311 in 1,613,894 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014679.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00152 AC: 232AN: 152186Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000438 AC: 110AN: 250870Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135664
GnomAD4 exome AF: 0.000182 AC: 266AN: 1461590Hom.: 3 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 727094
GnomAD4 genome AF: 0.00155 AC: 236AN: 152304Hom.: 2 Cov.: 32 AF XY: 0.00130 AC XY: 97AN XY: 74476
ClinVar
Submissions by phenotype
Mosaic variegated aneuploidy syndrome 2 Uncertain:1Benign:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
CEP57-related disorder Benign:1
This variant is classified as likely 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