15-20534332-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001145004.2(GOLGA6L6):c.2102G>A(p.Arg701Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R701W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145004.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA6L6 | NM_001145004.2 | c.2102G>A | p.Arg701Gln | missense_variant | 8/9 | ENST00000619213.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA6L6 | ENST00000619213.1 | c.2102G>A | p.Arg701Gln | missense_variant | 8/9 | 5 | NM_001145004.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 8AN: 122138Hom.: 0 Cov.: 16 FAILED QC
GnomAD3 exomes AF: 0.0000961 AC: 12AN: 124854Hom.: 0 AF XY: 0.0000594 AC XY: 4AN XY: 67298
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000635 AC: 78AN: 1228146Hom.: 0 Cov.: 25 AF XY: 0.0000474 AC XY: 29AN XY: 611926
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000654 AC: 8AN: 122246Hom.: 0 Cov.: 16 AF XY: 0.0000506 AC XY: 3AN XY: 59322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.2180G>A (p.R727Q) alteration is located in exon 8 (coding exon 8) of the GOLGA6L6 gene. This alteration results from a G to A substitution at nucleotide position 2180, causing the arginine (R) at amino acid position 727 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