chr15-28702369-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001282468.3(GOLGA8M):c.1568G>A(p.Gly523Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000808 in 1,380,934 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001282468.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA8M | NM_001282468.3 | c.1568G>A | p.Gly523Asp | missense_variant, splice_region_variant | 18/19 | ENST00000563027.2 | |
LOC107984746 | XR_001751465.2 | n.89+262C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA8M | ENST00000563027.2 | c.1568G>A | p.Gly523Asp | missense_variant, splice_region_variant | 18/19 | 5 | NM_001282468.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00101 AC: 145AN: 144000Hom.: 1 Cov.: 22
GnomAD3 exomes AF: 0.00134 AC: 178AN: 132924Hom.: 2 AF XY: 0.00149 AC XY: 108AN XY: 72336
GnomAD4 exome AF: 0.000808 AC: 1116AN: 1380934Hom.: 6 Cov.: 37 AF XY: 0.000844 AC XY: 575AN XY: 681388
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00101 AC: 145AN: 144100Hom.: 1 Cov.: 22 AF XY: 0.000869 AC XY: 61AN XY: 70156
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | GOLGA8M: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at