6-49526559-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001010904.2(GLYATL3):c.512G>A(p.Arg171Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,551,552 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001010904.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLYATL3 | NM_001010904.2 | c.512G>A | p.Arg171Gln | missense_variant | 6/6 | ENST00000371197.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLYATL3 | ENST00000371197.9 | c.512G>A | p.Arg171Gln | missense_variant | 6/6 | 2 | NM_001010904.2 | P1 | |
GLYATL3 | ENST00000545705.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000635 AC: 10AN: 157404Hom.: 0 AF XY: 0.0000481 AC XY: 4AN XY: 83226
GnomAD4 exome AF: 0.0000164 AC: 23AN: 1399344Hom.: 0 Cov.: 33 AF XY: 0.0000130 AC XY: 9AN XY: 690152
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.512G>A (p.R171Q) alteration is located in exon 6 (coding exon 5) of the GLYATL3 gene. This alteration results from a G to A substitution at nucleotide position 512, causing the arginine (R) at amino acid position 171 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