Genetic Variant NM_194318.4: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.

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