chr9-124911954-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002077.4(GOLGA1):c.916A>G(p.Arg306Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,611,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.916A>G | p.Arg306Gly | missense_variant | 11/23 | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.916A>G | p.Arg306Gly | missense_variant | 11/23 | 1 | NM_002077.4 | P1 | |
GOLGA1 | ENST00000485337.1 | c.244A>G | p.Arg82Gly | missense_variant, NMD_transcript_variant | 3/10 | 5 | |||
GOLGA1 | ENST00000475407.5 | c.*62A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/18 | 5 | ||||
GOLGA1 | ENST00000373551.4 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 48AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251460Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135900
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1459236Hom.: 0 Cov.: 29 AF XY: 0.0000262 AC XY: 19AN XY: 726162
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2022 | The c.916A>G (p.R306G) alteration is located in exon 11 (coding exon 9) of the GOLGA1 gene. This alteration results from a A to G substitution at nucleotide position 916, causing the arginine (R) at amino acid position 306 to be replaced by a glycine (G). 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