9-86035392-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016548.4(GOLM1):c.991G>A(p.Glu331Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016548.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOLM1 | ENST00000388712.7 | c.991G>A | p.Glu331Lys | missense_variant | Exon 8 of 10 | 1 | NM_016548.4 | ENSP00000373364.3 | ||
GOLM1 | ENST00000388711.7 | c.991G>A | p.Glu331Lys | missense_variant | Exon 8 of 10 | 1 | ENSP00000373363.3 | |||
GOLM1 | ENST00000257504.10 | n.*196G>A | downstream_gene_variant | 5 | ||||||
GOLM1 | ENST00000464314.1 | n.*3G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251206Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135792
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461744Hom.: 0 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 727160
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.991G>A (p.E331K) alteration is located in exon 8 (coding exon 7) of the GOLM1 gene. This alteration results from a G to A substitution at nucleotide position 991, causing the glutamic acid (E) at amino acid position 331 to be replaced by a lysine (K). 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