chr3-195213905-C-A

Position:

• chr3-195213905-C-A

Variant summary

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

The NM_152531.5(XXYLT1):​c.652+12804G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,212 control chromosomes in the GnomAD database, including 61,258 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 0.90 (61258 hom., cov: 31)
• Consequence: XXYLT1 NM_152531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XXYLT1	NM_152531.5	c.652+12804G>T		intron_variant		ENST00000310380.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XXYLT1	ENST00000310380.11	c.652+12804G>T		intron_variant		1	NM_152531.5	P1
XXYLT1	ENST00000429994.5	c.214+12804G>T		intron_variant		3
XXYLT1	ENST00000418940.5	c.215-6407G>T		intron_variant, NMD_transcript_variant		4
XXYLT1	ENST00000494175.1	n.216-6407G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136317 AN: 152094 Hom.: 61206 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.896 AC: 136427 AN: 152212 Hom.: 61258 Cov.: 31 AF XY: 0.894 AC XY: 66528 AN XY: 74408

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.910

Alfa AF: 0.883 Hom.: 71474

Bravo AF: 0.907

Asia WGS AF: 0.880 AC: 3062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.23

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: rs9825185; hg19: chr3-194934634;