rs4677655

chr3-195105408-C-T

Variant summary

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

The NM_152531.5(XXYLT1):c.786-35297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,008 control chromosomes in the GnomAD database, including 19,981 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 0.49 (19981 hom., cov: 33)
• Consequence: XXYLT1 NM_152531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

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]

LOC124909476 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XXYLT1	NM_152531.5	c.786-35297G>A		intron_variant		ENST00000310380.11
LOC124909476	XR_007096226.1	n.1136G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XXYLT1	ENST00000310380.11	c.786-35297G>A		intron_variant		1	NM_152531.5	P1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75104 AN: 151890 Hom.: 19975 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.494 AC: 75135 AN: 152008 Hom.: 19981 Cov.: 33 AF XY: 0.493 AC XY: 36628 AN XY: 74310

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.497

Alfa AF: 0.550 Hom.: 4793

Bravo AF: 0.484

Asia WGS AF: 0.241 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.8
Dann	Benign	0.72

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: rs4677655; hg19: chr3-194826137;