15-82344626-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001164465.3(GOLGA6L10):c.1234G>A(p.Glu412Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 148,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001164465.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOLGA6L10 | ENST00000610657.2 | c.1234G>A | p.Glu412Lys | missense_variant | 6/9 | 2 | NM_001164465.3 | ENSP00000479362.1 | ||
GOLGA6L10 | ENST00000621197.4 | c.985G>A | p.Glu329Lys | missense_variant | 7/10 | 5 | ENSP00000484254.2 |
Frequencies
GnomAD3 genomes AF: 0.0000675 AC: 10AN: 148114Hom.: 0 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000808 AC: 1131AN: 1400124Hom.: 0 Cov.: 36 AF XY: 0.000764 AC XY: 530AN XY: 693450
GnomAD4 genome AF: 0.0000675 AC: 10AN: 148114Hom.: 0 Cov.: 31 AF XY: 0.0000830 AC XY: 6AN XY: 72306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2024 | The c.1105G>A (p.E369K) alteration is located in exon 6 (coding exon 6) of the GOLGA6L10 gene. This alteration results from a G to A substitution at nucleotide position 1105, causing the glutamic acid (E) at amino acid position 369 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