rs117111131

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_194318.4(B3GLCT):c.271-12T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 1,597,596 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 38 hom., cov: 28)

Exomes 𝑓: 0.024 ( 541 hom. )

Consequence

B3GLCT
NM_194318.4 intron

Scores

Splicing: ADA: 0.00008837

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.256

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 13-31247011-T-C is Benign according to our data. Variant chr13-31247011-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 96625.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-31247011-T-C is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0186 (2812/151098) while in subpopulation NFE AF= 0.0263 (1787/67856). AF 95% confidence interval is 0.0253. There are 38 homozygotes in gnomad4. There are 1293 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 38 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4 link	c.271-12T>C		intron_variant	Intron 4 of 14	ENST00000343307.5	NP_919299.3	Q6Y288

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5 link	c.271-12T>C		intron_variant	Intron 4 of 14	1	NM_194318.4	ENSP00000343002.4		Q6Y288

Frequencies

GnomAD3 genomes

AF:

0.0186

AC:

2814

AN:

150988

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00526

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0216

Gnomad ASJ

AF:

0.0737

Gnomad EAS

AF:

0.000394

Gnomad SAS

AF:

0.00526

Gnomad FIN

AF:

0.0123

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0263

Gnomad OTH

AF:

0.0252

GnomAD3 exomes

AF:

0.0214

AC:

5368

AN:

251274

Hom.:

AF XY:

0.0217

AC XY:

2948

AN XY:

135796

show subpopulations

Gnomad AFR exome

AF:

0.00418

Gnomad AMR exome

AF:

0.0172

Gnomad ASJ exome

AF:

0.0718

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00817

Gnomad FIN exome

AF:

0.0160

Gnomad NFE exome

AF:

0.0282

Gnomad OTH exome

AF:

0.0294

GnomAD4 exome

AF:

0.0245

AC:

35404

AN:

1446498

Hom.:

541

Cov.:

AF XY:

0.0245

AC XY:

17636

AN XY:

720648

show subpopulations

Gnomad4 AFR exome

AF:

0.00488

Gnomad4 AMR exome

AF:

0.0176

Gnomad4 ASJ exome

AF:

0.0759

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.00786

Gnomad4 FIN exome

AF:

0.0159

Gnomad4 NFE exome

AF:

0.0266

Gnomad4 OTH exome

AF:

0.0258

GnomAD4 genome

AF:

0.0186

AC:

2812

AN:

151098

Hom.:

Cov.:

AF XY:

0.0175

AC XY:

1293

AN XY:

73802

show subpopulations

Gnomad4 AFR

AF:

0.00524

Gnomad4 AMR

AF:

0.0215

Gnomad4 ASJ

AF:

0.0737

Gnomad4 EAS

AF:

0.000395

Gnomad4 SAS

AF:

0.00527

Gnomad4 FIN

AF:

0.0123

Gnomad4 NFE

AF:

0.0263

Gnomad4 OTH

AF:

0.0249

Alfa

AF:

0.0274

Hom.:

Bravo

AF:

0.0199

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Peters plus syndrome

Benign:3

Jan 29, 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. -

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 18, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 05, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.020

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000088

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.17

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over