9-124899477-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002077.4(GOLGA1):c.1163C>T(p.Ala388Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000712 in 1,544,786 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/23 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_002077.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
GOLGA1 | NM_002077.4 | c.1163C>T | p.Ala388Val | missense_variant, splice_region_variant | 14/23 | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1163C>T | p.Ala388Val | missense_variant, splice_region_variant | 14/23 | 1 | NM_002077.4 | P1 | |
GOLGA1 | ENST00000475407.5 | c.*309C>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 9/18 | 5 | ||||
GOLGA1 | ENST00000485337.1 | c.417-44C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152232Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000371 AC: 57AN: 153752Hom.: 0 AF XY: 0.000379 AC XY: 31AN XY: 81790
GnomAD4 exome AF: 0.0000654 AC: 91AN: 1392436Hom.: 0 Cov.: 32 AF XY: 0.0000640 AC XY: 44AN XY: 687620
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152350Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at