9-124908406-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002077.4(GOLGA1):c.1036G>A(p.Ala346Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000348 in 1,609,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.1036G>A | p.Ala346Thr | missense_variant | 12/23 | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1036G>A | p.Ala346Thr | missense_variant | 12/23 | 1 | NM_002077.4 | P1 | |
GOLGA1 | ENST00000373551.4 | n.86G>A | non_coding_transcript_exon_variant | 2/3 | 5 | ||||
GOLGA1 | ENST00000485337.1 | c.364G>A | p.Ala122Thr | missense_variant, NMD_transcript_variant | 4/10 | 5 | |||
GOLGA1 | ENST00000475407.5 | c.*182G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251478Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135910
GnomAD4 exome AF: 0.0000371 AC: 54AN: 1457212Hom.: 0 Cov.: 28 AF XY: 0.0000400 AC XY: 29AN XY: 725316
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2021 | The c.1036G>A (p.A346T) alteration is located in exon 12 (coding exon 10) of the GOLGA1 gene. This alteration results from a G to A substitution at nucleotide position 1036, causing the alanine (A) at amino acid position 346 to be replaced by a threonine (T). 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