12-42087815-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173601.2(GXYLT1):c.1294C>A(p.Arg432Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000695 in 1,439,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173601.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GXYLT1 | NM_173601.2 | c.1294C>A | p.Arg432Ser | missense_variant | 8/8 | ENST00000398675.8 | |
GXYLT1 | NM_001099650.2 | c.1201C>A | p.Arg401Ser | missense_variant | 7/7 | ||
GXYLT1 | XM_017019211.1 | c.949C>A | p.Arg317Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GXYLT1 | ENST00000398675.8 | c.1294C>A | p.Arg432Ser | missense_variant | 8/8 | 1 | NM_173601.2 | P4 | |
GXYLT1 | ENST00000280876.6 | c.1201C>A | p.Arg401Ser | missense_variant | 7/7 | 1 | A1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1439010Hom.: 0 Cov.: 28 AF XY: 0.00000140 AC XY: 1AN XY: 715274
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.1294C>A (p.R432S) alteration is located in exon 8 (coding exon 8) of the GXYLT1 gene. This alteration results from a C to A substitution at nucleotide position 1294, causing the arginine (R) at amino acid position 432 to be replaced by a serine (S). 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.