X-30668097-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BS2_Supporting
The NM_001205019.2(GK):āc.238A>Gā(p.Ile80Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,031,362 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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_001205019.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000355 AC: 4AN: 112633Hom.: 0 Cov.: 23 AF XY: 0.0000575 AC XY: 2AN XY: 34755
GnomAD3 exomes AF: 0.0000930 AC: 17AN: 182744Hom.: 0 AF XY: 0.0000593 AC XY: 4AN XY: 67426
GnomAD4 exome AF: 0.0000185 AC: 17AN: 918676Hom.: 0 Cov.: 19 AF XY: 0.00000385 AC XY: 1AN XY: 259912
GnomAD4 genome AF: 0.0000355 AC: 4AN: 112686Hom.: 0 Cov.: 23 AF XY: 0.0000574 AC XY: 2AN XY: 34818
ClinVar
Submissions by phenotype
GK-related disorder Uncertain:1
The GK c.238A>G variant is predicted to result in the amino acid substitution p.Ile80Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.12% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-30686214-A-G). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at