13-31275394-C-T

Variant names:

• chr13-31275394-C-T
• rs877103
• NM_194318.4:c.780+766C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194318.4(B3GLCT):​c.780+766C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,074 control chromosomes in the GnomAD database, including 36,191 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (36191 hom., cov: 32)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• Peters plus syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet, G2P, PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.780+766C>T		intron_variant	Intron 9 of 14	ENST00000343307.5	NP_919299.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.780+766C>T		intron_variant	Intron 9 of 14	1	NM_194318.4	ENSP00000343002.4
B3GLCT	ENST00000461652.2	n.395+766C>T		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102323 AN: 151958 Hom.: 36187 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.707

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.673 AC: 102355 AN: 152074 Hom.: 36191 Cov.: 32 AF XY: 0.674 AC XY: 50079 AN XY: 74342

African (AFR) AF: 0.439 AC: 18213 AN: 41468

American (AMR) AF: 0.754 AC: 11513 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2874 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3859 AN: 5176

South Asian (SAS) AF: 0.763 AC: 3677 AN: 4818

European-Finnish (FIN) AF: 0.679 AC: 7174 AN: 10566

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.773 AC: 52521 AN: 67982

Other (OTH) AF: 0.708 AC: 1496 AN: 2114

Alfa AF: 0.712 Hom.: 7190

Bravo AF: 0.668

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs877103; hg19: chr13-31849531;