13-31232835-C-T

Variant names:

• chr13-31232835-C-T
• rs9315116
• NM_194318.4:c.270+3541C>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.270+3541C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 152,194 control chromosomes in the GnomAD database, including 1,538 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 0.090 (1538 hom., cov: 33)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 1 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194318.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	NM_194318.4	MANE Select	c.270+3541C>T		intron	N/A	NP_919299.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.270+3541C>T		intron	N/A	ENSP00000343002.4
	B3GLCT	ENST00000873566.1		c.270+3541C>T		intron	N/A	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.120+17735C>T		intron	N/A	ENSP00000616602.1

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13608 AN: 152076 Hom.: 1535 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00664

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0896 AC: 13641 AN: 152194 Hom.: 1538 Cov.: 33 AF XY: 0.0938 AC XY: 6978 AN XY: 74404

African (AFR) AF: 0.196 AC: 8134 AN: 41508

American (AMR) AF: 0.0874 AC: 1336 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2307 AN: 5162

South Asian (SAS) AF: 0.184 AC: 886 AN: 4822

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00664 AC: 452 AN: 68024

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0455 Hom.: 150

Bravo AF: 0.102

Asia WGS AF: 0.306 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.57
PhyloP100		0.65
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: rs9315116; hg19: chr13-31806972;