chr15-23443797-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001304388.2(GOLGA6L2):c.571T>C(p.Trp191Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 1,538,416 control chromosomes in the GnomAD database, including 559,609 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001304388.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA6L2 | NM_001304388.2 | c.571T>C | p.Trp191Arg | missense_variant | 5/8 | ENST00000567107.6 | |
GOLGA6L2 | XM_047432396.1 | c.412T>C | p.Trp138Arg | missense_variant | 3/6 | ||
GOLGA6L2 | XM_047432397.1 | c.571T>C | p.Trp191Arg | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA6L2 | ENST00000567107.6 | c.571T>C | p.Trp191Arg | missense_variant | 5/8 | 5 | NM_001304388.2 | P1 | |
GOLGA6L2 | ENST00000566571.5 | c.541T>C | p.Trp181Arg | missense_variant, NMD_transcript_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.808 AC: 122905AN: 152050Hom.: 50435 Cov.: 33
GnomAD3 exomes AF: 0.849 AC: 123093AN: 144922Hom.: 52504 AF XY: 0.849 AC XY: 66381AN XY: 78196
GnomAD4 exome AF: 0.856 AC: 1186717AN: 1386246Hom.: 509149 Cov.: 44 AF XY: 0.856 AC XY: 585598AN XY: 684288
GnomAD4 genome ? AF: 0.808 AC: 122978AN: 152170Hom.: 50460 Cov.: 33 AF XY: 0.811 AC XY: 60342AN XY: 74394
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at