NM_152531.5:c.786-31258A>G

Variant names:

• chr3-195101369-T-C
• rs952481
• NM_152531.5:c.786-31258A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152531.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XXYLT1	NM_152531.5	MANE Select	c.786-31258A>G		intron	N/A	NP_689744.3
	XXYLT1	NM_001308069.2		c.348-31258A>G		intron	N/A	NP_001294998.1
	XXYLT1	NM_001410854.1		c.177-31258A>G		intron	N/A	NP_001397783.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XXYLT1	ENST00000310380.11	TSL:1 MANE Select	c.786-31258A>G		intron	N/A	ENSP00000309640.6
	XXYLT1	ENST00000429994.5	TSL:3	c.348-31258A>G		intron	N/A	ENSP00000399422.1
	XXYLT1	ENST00000437101.5	TSL:2	c.177-31258A>G		intron	N/A	ENSP00000409865.1

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

African (AFR) AF: 0.261 AC: 10830 AN: 41552

American (AMR) AF: 0.183 AC: 2805 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2200 AN: 5172

South Asian (SAS) AF: 0.377 AC: 1820 AN: 4832

European-Finnish (FIN) AF: 0.189 AC: 2007 AN: 10594

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14288 AN: 68012

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.211 Hom.: 6667

Bravo AF: 0.227

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.032
DANN	Benign	0.75
PhyloP100		-2.1
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: rs952481; hg19: chr3-194822098;