9-86035593-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.790G>A(p.Glu264Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,078 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E264A) has been classified 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.790G>A | p.Glu264Lys | missense_variant | Exon 8 of 10 | 1 | NM_016548.4 | ENSP00000373364.3 | ||
GOLM1 | ENST00000388711.7 | c.790G>A | p.Glu264Lys | missense_variant | Exon 8 of 10 | 1 | ENSP00000373363.3 | |||
GOLM1 | ENST00000257504.10 | n.789G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | 5 | |||||
GOLM1 | ENST00000464314.1 | n.499G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453078Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 723284
GnomAD4 genome Cov.: 29
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.790G>A (p.E264K) 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 790, causing the glutamic acid (E) at amino acid position 264 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
Publications
No publications associated with this variant yet.