chr16-17470643-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_022166.4(XYLT1):c.154G>A(p.Gly52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,111,762 control chromosomes in the GnomAD database, including 7 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022166.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT1 | NM_022166.4 | c.154G>A | p.Gly52Ser | missense_variant | 1/12 | ENST00000261381.7 | |
XYLT1 | XM_047434458.1 | c.154G>A | p.Gly52Ser | missense_variant | 1/11 | ||
XYLT1 | XM_017023539.3 | c.154G>A | p.Gly52Ser | missense_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT1 | ENST00000261381.7 | c.154G>A | p.Gly52Ser | missense_variant | 1/12 | 1 | NM_022166.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000913 AC: 134AN: 146762Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.00119 AC: 49AN: 41118Hom.: 0 AF XY: 0.00120 AC XY: 30AN XY: 24930
GnomAD4 exome AF: 0.00142 AC: 1367AN: 964890Hom.: 6 Cov.: 29 AF XY: 0.00144 AC XY: 669AN XY: 466032
GnomAD4 genome AF: 0.000912 AC: 134AN: 146872Hom.: 1 Cov.: 30 AF XY: 0.000867 AC XY: 62AN XY: 71498
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Has not been previously published as pathogenic or benign to our knowledge - |
Desbuquois dysplasia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
XYLT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at