13-31247103-C-T

Variant names:

• chr13-31247103-C-T
• rs9564692
• NM_194318.4:c.347+4C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_194318.4(B3GLCT):​c.347+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,607,250 control chromosomes in the GnomAD database, including 98,488 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.36 (10798 hom., cov: 29)
  • Exomes 𝑓: 0.33 (87690 hom.)
• Consequence: B3GLCT NM_194318.4 splice_region, intron
• Scores: Splicing: ADA: 0.0001060
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 0.0350

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 13-31247103-C-T is Benign according to our data. Variant chr13-31247103-C-T is described in ClinVar as [Benign]. Clinvar id is 96627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-31247103-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.347+4C>T		splice_region_variant, intron_variant	Intron 5 of 14	ENST00000343307.5	NP_919299.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.347+4C>T		splice_region_variant, intron_variant	Intron 5 of 14	1	NM_194318.4	ENSP00000343002.4

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55089 AN: 151710 Hom.: 10777 Cov.: 29

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.371

GnomAD3 exomes AF: 0.404 AC: 101516 AN: 251078 Hom.: 23111 AF XY: 0.399 AC XY: 54108 AN XY: 135702

Gnomad AFR exome AF: 0.396

Gnomad AMR exome AF: 0.560

Gnomad ASJ exome AF: 0.461

Gnomad EAS exome AF: 0.742

Gnomad SAS exome AF: 0.487

Gnomad FIN exome AF: 0.307

Gnomad NFE exome AF: 0.296

Gnomad OTH exome AF: 0.374

GnomAD4 exome AF: 0.331 AC: 482289 AN: 1455422 Hom.: 87690 Cov.: 33 AF XY: 0.336 AC XY: 243137 AN XY: 724420

Gnomad4 AFR exome AF: 0.399

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.469

Gnomad4 EAS exome AF: 0.723

Gnomad4 SAS exome AF: 0.482

Gnomad4 FIN exome AF: 0.301

Gnomad4 NFE exome AF: 0.291

Gnomad4 OTH exome AF: 0.359

GnomAD4 genome AF: 0.363 AC: 55145 AN: 151828 Hom.: 10798 Cov.: 29 AF XY: 0.370 AC XY: 27440 AN XY: 74160

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.374

Alfa AF: 0.324 Hom.: 3594

Bravo AF: 0.379

Asia WGS AF: 0.609 AC: 2113 AN: 3478

EpiCase AF: 0.296

EpiControl AF: 0.305

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Peters plus syndrome Benign:3

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not specified Benign:2

Jul 03, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.8
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00011
dbscSNV1_RF	Benign	0.016
SpliceAI score (max)		0.36		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.36		Position offset: -4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9564692; hg19: chr13-31821240;