rs9315120

Positions:

• chr13-31249452-G-A

Variant summary

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

The ENST00000343307.5(B3GLCT):​c.459+1486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,000 control chromosomes in the GnomAD database, including 8,816 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 0.32 (8816 hom., cov: 32)
• Consequence: B3GLCT ENST00000343307.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661

Genes affected

B3GLCT (HGNC:20207): (beta 3-glucosyltransferase) The protein encoded by this gene is a beta-1,3-glucosyltransferase that transfers glucose to O-linked fucosylglycans on thrombospondin type-1 repeats (TSRs) of several proteins. The encoded protein is a type II membrane protein. Defects in this gene are a cause of Peters-plus syndrome (PPS).[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.459+1486G>A		intron_variant		ENST00000343307.5	NP_919299.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.459+1486G>A		intron_variant		1	NM_194318.4	ENSP00000343002	P1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48385 AN: 151882 Hom.: 8817 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.318 AC: 48377 AN: 152000 Hom.: 8816 Cov.: 32 AF XY: 0.311 AC XY: 23113 AN XY: 74262

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.320

Alfa AF: 0.399 Hom.: 25289

Bravo AF: 0.309

Asia WGS AF: 0.0890 AC: 312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.65

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: rs9315120; hg19: chr13-31823589;