rs770553728
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001001995.3(GPM6B):c.509G>A(p.Arg170Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000048 in 1,188,684 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 25 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001995.3 missense
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: 0.0000446 AC: 5AN: 112141Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34295
GnomAD3 exomes AF: 0.0000314 AC: 5AN: 159345Hom.: 0 AF XY: 0.0000415 AC XY: 2AN XY: 48227
GnomAD4 exome AF: 0.0000483 AC: 52AN: 1076543Hom.: 0 Cov.: 28 AF XY: 0.0000721 AC XY: 25AN XY: 346799
GnomAD4 genome AF: 0.0000446 AC: 5AN: 112141Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34295
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.509G>A (p.R170Q) alteration is located in exon 4 (coding exon 4) of the GPM6B gene. This alteration results from a G to A substitution at nucleotide position 509, causing the arginine (R) at amino acid position 170 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