rs4677655

Variant names:

• chr3-195105408-C-T
• rs4677655
• NM_152531.5:c.786-35297G>A

Variant summary

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

The NM_152531.5(XXYLT1):​c.786-35297G>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
• Publications: 2 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]

LOC124909476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XXYLT1	NM_152531.5	MANE Select	c.786-35297G>A		intron	N/A	NP_689744.3
	XXYLT1	NM_001308069.2		c.348-35297G>A		intron	N/A	NP_001294998.1	A0A140T9D0
	XXYLT1	NM_001410854.1		c.177-35297G>A		intron	N/A	NP_001397783.1	Q8NBI6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XXYLT1	ENST00000310380.11	TSL:1 MANE Select	c.786-35297G>A		intron	N/A	ENSP00000309640.6	Q8NBI6-1
	XXYLT1	ENST00000429994.5	TSL:3	c.348-35297G>A		intron	N/A	ENSP00000399422.1	A0A140T9D0
	XXYLT1	ENST00000437101.5	TSL:2	c.177-35297G>A		intron	N/A	ENSP00000409865.1	Q8NBI6-2

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

African (AFR) AF: 0.358 AC: 14846 AN: 41444

American (AMR) AF: 0.546 AC: 8354 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1975 AN: 3464

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5174

South Asian (SAS) AF: 0.379 AC: 1826 AN: 4818

European-Finnish (FIN) AF: 0.640 AC: 6769 AN: 10570

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39410 AN: 67932

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.84
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: rs4677655; hg19: chr3-194826137;