rs9542236

Variant names:

• chr13-31245188-T-C
• rs9542236
• NM_194318.4:c.271-1835T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

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]

B3GLCT Gene-Disease associations (from GenCC):

• Peters plus syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194318.4. 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
	B3GLCT	NM_194318.4	MANE Select	c.271-1835T>C		intron	N/A	NP_919299.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.271-1835T>C		intron	N/A	ENSP00000343002.4	Q6Y288
	B3GLCT	ENST00000873566.1		c.271-15758T>C		intron	N/A	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.121-15758T>C		intron	N/A	ENSP00000616602.1

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

African (AFR) AF: 0.227 AC: 9416 AN: 41464

American (AMR) AF: 0.309 AC: 4712 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5188

South Asian (SAS) AF: 0.174 AC: 837 AN: 4820

European-Finnish (FIN) AF: 0.374 AC: 3947 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29839 AN: 67938

Other (OTH) AF: 0.336 AC: 709 AN: 2112

Alfa AF: 0.391 Hom.: 17802

Bravo AF: 0.330

Asia WGS AF: 0.0960 AC: 334 AN: 3476

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.8
DANN	Benign	0.78
PhyloP100		0.72
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: rs9542236; hg19: chr13-31819325;