rs9542236

chr13-31245188-T-C

Variant summary

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

The NM_194318.4(B3GLCT):c.271-1835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,028 control chromosomes in the GnomAD database, including 9,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.34 (9726 hom., cov: 32)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.718

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GLCT	NM_194318.4	c.271-1835T>C		intron_variant		ENST00000343307.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GLCT	ENST00000343307.5	c.271-1835T>C		intron_variant		1	NM_194318.4	P1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51430 AN: 151910 Hom.: 9728 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.338 AC: 51427 AN: 152028 Hom.: 9726 Cov.: 32 AF XY: 0.330 AC XY: 24513 AN XY: 74316

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.336

Alfa AF: 0.370 Hom.: 1277

Bravo AF: 0.330

Asia WGS AF: 0.0960 AC: 334 AN: 3476

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	4.8
Dann	Benign	0.78

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: rs9542236; hg19: chr13-31819325;