9-124889223-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.1681G>A(p.Ala561Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,082 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GOLGA1 | NM_002077.4 | c.1681G>A | p.Ala561Thr | missense_variant | Exon 18 of 23 | ENST00000373555.9 | NP_002068.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1681G>A | p.Ala561Thr | missense_variant | Exon 18 of 23 | 1 | NM_002077.4 | ENSP00000362656.4 | ||
GOLGA1 | ENST00000485337.1 | n.*435G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 5 | ENSP00000435006.1 | ||||
GOLGA1 | ENST00000485337.1 | n.*435G>A | 3_prime_UTR_variant | Exon 10 of 10 | 5 | ENSP00000435006.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461082Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726872
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1681G>A (p.A561T) alteration is located in exon 18 (coding exon 16) of the GOLGA1 gene. This alteration results from a G to A substitution at nucleotide position 1681, causing the alanine (A) at amino acid position 561 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
Publications
No publications associated with this variant yet.