13-31275434-A-C

Variant names:

• chr13-31275434-A-C
• rs877104
• NM_194318.4:c.780+806A>C

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+806A>C 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 152,022 control chromosomes in the GnomAD database, including 36,161 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 (36161 hom., cov: 31)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 9 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	NM_194318.4	MANE Select	c.780+806A>C		intron	N/A	NP_919299.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.780+806A>C		intron	N/A	ENSP00000343002.4
	B3GLCT	ENST00000461652.2	TSL:3	n.395+806A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102265 AN: 151904 Hom.: 36157 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.673 AC: 102298 AN: 152022 Hom.: 36161 Cov.: 31 AF XY: 0.673 AC XY: 50041 AN XY: 74304

African (AFR) AF: 0.439 AC: 18174 AN: 41426

American (AMR) AF: 0.754 AC: 11513 AN: 15278

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

East Asian (EAS) AF: 0.744 AC: 3840 AN: 5160

South Asian (SAS) AF: 0.762 AC: 3673 AN: 4818

European-Finnish (FIN) AF: 0.679 AC: 7181 AN: 10580

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52519 AN: 67972

Other (OTH) AF: 0.707 AC: 1494 AN: 2112

Alfa AF: 0.747 Hom.: 21934

Bravo AF: 0.668

Asia WGS AF: 0.768 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		0.19
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: rs877104; hg19: chr13-31849571;