15-23129919-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001001413.3(GOLGA6L1):c.1534C>T(p.Arg512Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 119,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001413.3 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: 0.000494 AC: 59AN: 119330Hom.: 0 Cov.: 25
GnomAD3 exomes AF: 0.0000734 AC: 10AN: 136190Hom.: 3 AF XY: 0.0000551 AC XY: 4AN XY: 72644
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000697 AC: 430AN: 617100Hom.: 0 Cov.: 8 AF XY: 0.000644 AC XY: 210AN XY: 326014
GnomAD4 genome AF: 0.000494 AC: 59AN: 119416Hom.: 0 Cov.: 25 AF XY: 0.000491 AC XY: 28AN XY: 57012
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1534C>T (p.R512W) alteration is located in exon 8 (coding exon 8) of the GOLGA6L1 gene. This alteration results from a C to T substitution at nucleotide position 1534, causing the arginine (R) at amino acid position 512 to be replaced by a tryptophan (W). 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