2-190910319-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS1_Supporting
The NM_014905.5(GLS):āc.1036A>Cā(p.Lys346Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000226 in 1,558,422 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014905.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 29AN: 242376Hom.: 0 AF XY: 0.000107 AC XY: 14AN XY: 131212
GnomAD4 exome AF: 0.000236 AC: 332AN: 1406260Hom.: 1 Cov.: 22 AF XY: 0.000217 AC XY: 152AN XY: 701922
GnomAD4 genome AF: 0.000131 AC: 20AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74328
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1036A>C (p.K346Q) alteration is located in exon 7 (coding exon 7) of the GLS gene. This alteration results from a A to C substitution at nucleotide position 1036, causing the lysine (K) at amino acid position 346 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at