13-31215032-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

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
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.182

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 -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	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GLCT	NM_194318.4	c.71-5del		intron_variant		ENST00000343307.5
B3GLCT	XM_006719768.4	c.14-5del		intron_variant
B3GLCT	XM_011534936.2	c.71-5del		intron_variant
B3GLCT	XM_047430111.1	c.71-5del		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.952 AC: 138966 AN: 146006 Hom.: 66218 Cov.: 0

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

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.: 0 AF XY: 0.569 AC XY: 316986 AN XY: 556834

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.: 0 AF XY: 0.953 AC XY: 67547 AN XY: 70878

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

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

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: rs398022187; hg19: chr13-31789169;