3-72888505-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080393.2(GXYLT2):c.272C>T(p.Ala91Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000243 in 1,235,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080393.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151466Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000185 AC: 2AN: 1083752Hom.: 0 Cov.: 30 AF XY: 0.00000192 AC XY: 1AN XY: 521720
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151466Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73950
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.272C>T (p.A91V) alteration is located in exon 1 (coding exon 1) of the GXYLT2 gene. This alteration results from a C to T substitution at nucleotide position 272, causing the alanine (A) at amino acid position 91 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