9-124908423-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.1019C>T(p.Ala340Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,611,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.1019C>T | p.Ala340Val | missense_variant | 12/23 | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1019C>T | p.Ala340Val | missense_variant | 12/23 | 1 | NM_002077.4 | P1 | |
GOLGA1 | ENST00000373551.4 | n.69C>T | non_coding_transcript_exon_variant | 2/3 | 5 | ||||
GOLGA1 | ENST00000485337.1 | c.347C>T | p.Ala116Val | missense_variant, NMD_transcript_variant | 4/10 | 5 | |||
GOLGA1 | ENST00000475407.5 | c.*165C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251472Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135906
GnomAD4 exome AF: 0.000138 AC: 201AN: 1458914Hom.: 0 Cov.: 28 AF XY: 0.000125 AC XY: 91AN XY: 725994
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.1019C>T (p.A340V) alteration is located in exon 12 (coding exon 10) of the GOLGA1 gene. This alteration results from a C to T substitution at nucleotide position 1019, causing the alanine (A) at amino acid position 340 to be replaced by a valine (V). 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