chr17-50346155-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_022167.4(XYLT2):c.15G>A(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000664 in 1,267,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00066 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00066 ( 0 hom. )
Consequence
XYLT2
NM_022167.4 synonymous
NM_022167.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.0200
Genes affected
XYLT2 (HGNC:15517): (xylosyltransferase 2) The protein encoded by this gene is an isoform of xylosyltransferase, which belongs to a family of glycosyltransferases. This enzyme transfers xylose from UDP-xylose to specific serine residues of the core protein and initiates the biosynthesis of glycosaminoglycan chains in proteoglycans including chondroitin sulfate, heparan sulfate, heparin and dermatan sulfate. The enzyme activity, which is increased in scleroderma patients, is a diagnostic marker for the determination of sclerotic activity in systemic sclerosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 17-50346155-G-A is Benign according to our data. Variant chr17-50346155-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1664871.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.02 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000656 (97/147922) while in subpopulation NFE AF= 0.00128 (85/66352). AF 95% confidence interval is 0.00106. There are 1 homozygotes in gnomad4. There are 42 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT2 | NM_022167.4 | c.15G>A | p.Ala5= | synonymous_variant | 1/11 | ENST00000017003.7 | |
XYLT2 | NR_110010.2 | n.30G>A | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT2 | ENST00000017003.7 | c.15G>A | p.Ala5= | synonymous_variant | 1/11 | 1 | NM_022167.4 | P1 | |
XYLT2 | ENST00000376550.7 | c.15G>A | p.Ala5= | synonymous_variant, NMD_transcript_variant | 1/10 | 1 | |||
XYLT2 | ENST00000507602.5 | c.15G>A | p.Ala5= | synonymous_variant | 1/10 | 2 | |||
XYLT2 | ENST00000509778.1 | c.15G>A | p.Ala5= | synonymous_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000656 AC: 97AN: 147922Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000428 AC: 34AN: 79514Hom.: 0 AF XY: 0.000354 AC XY: 16AN XY: 45242
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GnomAD4 exome AF: 0.000665 AC: 744AN: 1119252Hom.: 0 Cov.: 30 AF XY: 0.000650 AC XY: 358AN XY: 551014
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GnomAD4 genome AF: 0.000656 AC: 97AN: 147922Hom.: 1 Cov.: 32 AF XY: 0.000583 AC XY: 42AN XY: 72014
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at