3-195137645-G-A

Variant names:

• chr3-195137645-G-A
• rs2131877
• NM_152531.5:c.785+18804C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152531.5(XXYLT1):​c.785+18804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,110 control chromosomes in the GnomAD database, including 3,834 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 0.21 (3834 hom., cov: 32)
• Consequence: XXYLT1 NM_152531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 46 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XXYLT1	NM_152531.5	c.785+18804C>T		intron_variant	Intron 3 of 3	ENST00000310380.11	NP_689744.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XXYLT1	ENST00000310380.11	c.785+18804C>T		intron_variant	Intron 3 of 3	1	NM_152531.5	ENSP00000309640.6

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31670 AN: 151992 Hom.: 3822 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.208 AC: 31715 AN: 152110 Hom.: 3834 Cov.: 32 AF XY: 0.211 AC XY: 15679 AN XY: 74374

African (AFR) AF: 0.212 AC: 8795 AN: 41492

American (AMR) AF: 0.225 AC: 3435 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2919 AN: 5176

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1348 AN: 10572

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.180 AC: 12203 AN: 67982

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.200 Hom.: 11068

Bravo AF: 0.215

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2131877; hg19: chr3-194858374;