15-20534506-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001145004.2(GOLGA6L6):c.1928C>T(p.Thr643Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000344 in 1,129,454 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145004.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000459 AC: 17AN: 37060Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.000226 AC: 33AN: 145878Hom.: 4 AF XY: 0.000245 AC XY: 19AN XY: 77540
GnomAD4 exome AF: 0.000341 AC: 372AN: 1092394Hom.: 18 Cov.: 47 AF XY: 0.000345 AC XY: 183AN XY: 530248
GnomAD4 genome AF: 0.000459 AC: 17AN: 37060Hom.: 0 Cov.: 0 AF XY: 0.000323 AC XY: 6AN XY: 18562
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2006C>T (p.T669M) alteration is located in exon 8 (coding exon 8) of the GOLGA6L6 gene. This alteration results from a C to T substitution at nucleotide position 2006, causing the threonine (T) at amino acid position 669 to be replaced by a methionine (M). 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