7-158646554-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_017760.7(NCAPG2):c.3085G>A(p.Val1029Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,571,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017760.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000279 AC: 57AN: 204562Hom.: 0 AF XY: 0.000284 AC XY: 32AN XY: 112616
GnomAD4 exome AF: 0.000149 AC: 211AN: 1418930Hom.: 0 Cov.: 30 AF XY: 0.000164 AC XY: 116AN XY: 705882
GnomAD4 genome AF: 0.000223 AC: 34AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign: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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at