rs952481

chr3-195101369-T-C

Variant summary

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

The NM_152531.5(XXYLT1):c.786-31258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,248 control chromosomes in the GnomAD database, including 4,240 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 0.23 (4240 hom., cov: 32)
• Consequence: XXYLT1 NM_152531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

XXYLT1 (HGNC:26639): (xyloside xylosyltransferase 1) Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in O-glycan processing. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XXYLT1	NM_152531.5	c.786-31258A>G		intron_variant		ENST00000310380.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XXYLT1	ENST00000310380.11	c.786-31258A>G		intron_variant		1	NM_152531.5	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35088 AN: 152130 Hom.: 4240 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.231 AC: 35113 AN: 152248 Hom.: 4240 Cov.: 32 AF XY: 0.231 AC XY: 17212 AN XY: 74428

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.234

Alfa AF: 0.207 Hom.: 4630

Bravo AF: 0.227

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.032
Dann	Benign	0.75

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: rs952481; hg19: chr3-194822098;