rs9933117

chr16-17161714-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022166.4(XYLT1):c.1290-2805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 150,738 control chromosomes in the GnomAD database, including 35,388 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (35388 hom., cov: 29)
• Consequence: XYLT1 NM_022166.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

Genes affected

XYLT1 (HGNC:15516): (xylosyltransferase 1) This locus encodes a xylosyltransferase enzyme. The encoded protein catalyzes transfer of UDP-xylose to serine residues of an acceptor protein substrate. This transfer reaction is necessary for biosynthesis of glycosaminoglycan chains. Mutations in this gene have been associated with increased severity of pseudoxanthoma elasticum.[provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XYLT1	NM_022166.4	c.1290-2805A>G		intron_variant		ENST00000261381.7
XYLT1	XM_017023539.3	c.1290-2805A>G		intron_variant
XYLT1	XM_047434458.1	c.1251-2805A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XYLT1	ENST00000261381.7	c.1290-2805A>G		intron_variant		1	NM_022166.4	P1

Frequencies

GnomAD3 genomes AF: 0.682 AC: 102784 AN: 150618 Hom.: 35384 Cov.: 29

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.687

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.682 AC: 102813 AN: 150738 Hom.: 35388 Cov.: 29 AF XY: 0.676 AC XY: 49680 AN XY: 73544

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.689

Alfa AF: 0.718 Hom.: 38180

Bravo AF: 0.671

Asia WGS AF: 0.607 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.022
Dann	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9933117; hg19: chr16-17255571;