rs13080

Variant names:

• chr13-31332004-A-C
• rs13080
• NM_194318.4:c.*2336A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-31332004-A-C
• chr13-31332004-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_194318.4(B3GLCT):​c.*2336A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,002 control chromosomes in the GnomAD database, including 35,149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.67 (35149 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: B3GLCT NM_194318.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.52
• Publications: 22 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 13-31332004-A-C is Benign according to our data. Variant chr13-31332004-A-C is described in ClinVar as Benign. ClinVar VariationId is 880658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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.*2336A>C		3_prime_UTR	Exon 15 of 15	NP_919299.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.*2336A>C		3_prime_UTR	Exon 15 of 15	ENSP00000343002.4

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101738 AN: 151884 Hom.: 35149 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.676

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.670 AC: 101780 AN: 152002 Hom.: 35149 Cov.: 32 AF XY: 0.665 AC XY: 49431 AN XY: 74306

African (AFR) AF: 0.500 AC: 20732 AN: 41450

American (AMR) AF: 0.691 AC: 10560 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2629 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2954 AN: 5160

South Asian (SAS) AF: 0.656 AC: 3161 AN: 4816

European-Finnish (FIN) AF: 0.684 AC: 7227 AN: 10568

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52070 AN: 67952

Other (OTH) AF: 0.673 AC: 1418 AN: 2106

Alfa AF: 0.728 Hom.: 108017

Bravo AF: 0.664

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	Peters plus syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.56
PhyloP100		-2.5
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: rs13080; hg19: chr13-31906141;