Genetic Variant B3GLCT:c.71-6_71-5delTT (chr13-31215032-CTT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_194318.4(B3GLCT):c.71-6_71-5delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.066 in 1,071,834 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.076 ( 0 hom. )

Consequence

B3GLCT
NM_194318.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.772

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 -10 ACMG points.

BP6

Variant 13-31215032-CTT-C is Benign according to our data. Variant chr13-31215032-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1227558.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-31215032-CTT-C is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4 link	c.71-6_71-5delTT	splice_region_variant, intron_variant	Intron 1 of 14	ENST00000343307.5	NP_919299.3	Q6Y288
B3GLCT	XM_006719768.4 link	c.14-6_14-5delTT	splice_region_variant, intron_variant	Intron 1 of 14		XP_006719831.1
B3GLCT	XM_011534936.2 link	c.71-6_71-5delTT	splice_region_variant, intron_variant	Intron 1 of 13		XP_011533238.1
B3GLCT	XM_047430111.1 link	c.71-6_71-5delTT	splice_region_variant, intron_variant	Intron 1 of 11		XP_047286067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5 link	c.71-18_71-17delTT		intron_variant	Intron 1 of 14	1	NM_194318.4	ENSP00000343002.4		Q6Y288

Frequencies

GnomAD3 genomes

AF:

0.00146

AC:

213

AN:

145804

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00245

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00116

Gnomad ASJ

AF:

0.000589

Gnomad EAS

AF:

0.000398

Gnomad SAS

AF:

0.000217

Gnomad FIN

AF:

0.00540

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000636

Gnomad OTH

AF:

0.00150

GnomAD3 exomes

AF:

0.144

AC:

18801

AN:

130932

Hom.:

AF XY:

0.148

AC XY:

10431

AN XY:

70650

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.133

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.137

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.0762

AC:

70563

AN:

925962

Hom.:

AF XY:

0.0774

AC XY:

35549

AN XY:

459514

show subpopulations

Gnomad4 AFR exome

AF:

0.0605

Gnomad4 AMR exome

AF:

0.124

Gnomad4 ASJ exome

AF:

0.0950

Gnomad4 EAS exome

AF:

0.0853

Gnomad4 SAS exome

AF:

0.0929

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.0716

Gnomad4 OTH exome

AF:

0.0767

GnomAD4 genome

AF:

0.00148

AC:

216

AN:

145872

Hom.:

Cov.:

AF XY:

0.00171

AC XY:

121

AN XY:

70746

show subpopulations

Gnomad4 AFR

AF:

0.00245

Gnomad4 AMR

AF:

0.00116

Gnomad4 ASJ

AF:

0.000589

Gnomad4 EAS

AF:

0.000599

Gnomad4 SAS

AF:

0.000654

Gnomad4 FIN

AF:

0.00540

Gnomad4 NFE

AF:

0.000636

Gnomad4 OTH

AF:

0.00149

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 04, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

13-31215032-CTTTTTT-CTTTT

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