rs61758388
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022166.4(XYLT1):c.343G>T(p.Ala115Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0268 in 1,230,650 control chromosomes in the GnomAD database, including 523 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022166.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XYLT1 | NM_022166.4 | c.343G>T | p.Ala115Ser | missense_variant | Exon 1 of 12 | ENST00000261381.7 | NP_071449.1 | |
XYLT1 | XM_047434458.1 | c.343G>T | p.Ala115Ser | missense_variant | Exon 1 of 11 | XP_047290414.1 | ||
XYLT1 | XM_017023539.3 | c.343G>T | p.Ala115Ser | missense_variant | Exon 1 of 12 | XP_016879028.1 | ||
LOC107987234 | XR_001752091.2 | n.-27G>T | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0187 AC: 2845AN: 151840Hom.: 49 Cov.: 31
GnomAD3 exomes AF: 0.0273 AC: 27AN: 988Hom.: 0 AF XY: 0.0234 AC XY: 13AN XY: 556
GnomAD4 exome AF: 0.0280 AC: 30184AN: 1078696Hom.: 474 Cov.: 30 AF XY: 0.0279 AC XY: 14220AN XY: 510138
GnomAD4 genome AF: 0.0187 AC: 2844AN: 151954Hom.: 49 Cov.: 31 AF XY: 0.0177 AC XY: 1313AN XY: 74270
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is associated with the following publications: (PMID: 19014925, 16759312, 16571645) -
Desbuquois dysplasia 2 Benign:1
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Desbuquois dysplasia 1 Benign:1
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PSEUDOXANTHOMA ELASTICUM, MODIFIER OF SEVERITY OF Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at