Variant 13-31215032-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_194318.4(B3GLCT):c.71-5del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 66214 hom., cov: 0)

Exomes 𝑓: 0.57 ( 79488 hom. )

Failed GnomAD Quality Control

Consequence

B3GLCT
NM_194318.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.182

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 13-31215032-CT-C is Benign according to our data. Variant chr13-31215032-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 166716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-31215032-CT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
B3GLCT	NM_194318.4 linkuse as main transcript	c.71-5del	intron_variant	ENST00000343307.5
B3GLCT	XM_006719768.4 linkuse as main transcript	c.14-5del	intron_variant
B3GLCT	XM_011534936.2 linkuse as main transcript	c.71-5del	intron_variant
B3GLCT	XM_047430111.1 linkuse as main transcript	c.71-5del	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GLCT	ENST00000343307.5 linkuse as main transcript	c.71-5del		intron_variant		1	NM_194318.4	P1

Frequencies

GnomAD3 genomes

AF:

0.952

AC:

138966

AN:

146006

Hom.:

66218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.888

Gnomad AMI

AF:

0.986

Gnomad AMR

AF:

0.972

Gnomad ASJ

AF:

0.990

Gnomad EAS

AF:

0.992

Gnomad SAS

AF:

0.990

Gnomad FIN

AF:

0.963

Gnomad MID

AF:

0.967

Gnomad NFE

AF:

0.976

Gnomad OTH

AF:

0.960

GnomAD3 exomes

AF:

0.590

AC:

77203

AN:

130932

Hom.:

11823

AF XY:

0.584

AC XY:

41271

AN XY:

70650

show subpopulations

Gnomad AFR exome

AF:

0.578

Gnomad AMR exome

AF:

0.571

Gnomad ASJ exome

AF:

0.556

Gnomad EAS exome

AF:

0.590

Gnomad SAS exome

AF:

0.554

Gnomad FIN exome

AF:

0.660

Gnomad NFE exome

AF:

0.599

Gnomad OTH exome

AF:

0.577

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.571

AC:

633696

AN:

1109860

Hom.:

79488

Cov.:

AF XY:

0.569

AC XY:

316986

AN XY:

556834

show subpopulations

Gnomad4 AFR exome

AF:

0.548

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.557

Gnomad4 SAS exome

AF:

0.552

Gnomad4 FIN exome

AF:

0.573

Gnomad4 NFE exome

AF:

0.575

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.952

AC:

138993

AN:

146074

Hom.:

66214

Cov.:

AF XY:

0.953

AC XY:

67547

AN XY:

70878

show subpopulations

Gnomad4 AFR

AF:

0.887

Gnomad4 AMR

AF:

0.972

Gnomad4 ASJ

AF:

0.990

Gnomad4 EAS

AF:

0.992

Gnomad4 SAS

AF:

0.989

Gnomad4 FIN

AF:

0.963

Gnomad4 NFE

AF:

0.976

Gnomad4 OTH

AF:

0.959

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Feb 28, 2014

- -

Peters plus syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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