chr9-124898590-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002077.4(GOLGA1):c.1366C>T(p.Arg456Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00018 in 1,609,926 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002077.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA1 | NM_002077.4 | c.1366C>T | p.Arg456Cys | missense_variant | 15/23 | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1366C>T | p.Arg456Cys | missense_variant | 15/23 | 1 | NM_002077.4 | P1 | |
GOLGA1 | ENST00000475407.5 | c.*512C>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/18 | 5 | ||||
GOLGA1 | ENST00000485337.1 | c.*120C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000267 AC: 67AN: 250936Hom.: 0 AF XY: 0.000332 AC XY: 45AN XY: 135616
GnomAD4 exome AF: 0.000179 AC: 261AN: 1457760Hom.: 1 Cov.: 28 AF XY: 0.000186 AC XY: 135AN XY: 725418
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.1366C>T (p.R456C) alteration is located in exon 15 (coding exon 13) of the GOLGA1 gene. This alteration results from a C to T substitution at nucleotide position 1366, causing the arginine (R) at amino acid position 456 to be replaced by a cysteine (C). 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