chr13-31215032-CT-C

Variant names:

• chr13-31215032-CT-C
• rs398022187
• NM_194318.4:c.71-5delT

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_194318.4(B3GLCT):​c.71-5delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.95 (66214 hom., cov: 0)
  • Exomes 𝑓: 0.57 (79488 hom.)
  • Failed GnomAD Quality Control
• Consequence: B3GLCT NM_194318.4 splice_region, intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.182
• Publications: 3 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: PanelApp Australia, Orphanet, G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant 13-31215032-CT-C is Benign according to our data. Variant chr13-31215032-CT-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 166716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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.71-5delT		splice_region 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.71-18delT		intron	N/A	ENSP00000343002.4	Q6Y288
	B3GLCT	ENST00000873566.1		c.71-18delT		intron	N/A	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.71-18delT		intron	N/A	ENSP00000616602.1

Frequencies

GnomAD3 genomes AF: 0.952 AC: 138966 AN: 146006 Hom.: 66218 Cov.: 0

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.967

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.960

GnomAD2 exomes AF: 0.590 AC: 77203 AN: 130932 AF XY: 0.584

Gnomad AFR exome AF: 0.578

Gnomad AMR exome AF: 0.571

Gnomad ASJ exome AF: 0.556

Gnomad EAS exome AF: 0.590

Gnomad FIN exome AF: 0.660

Gnomad NFE exome AF: 0.599

Gnomad OTH exome AF: 0.577

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.571 AC: 633696 AN: 1109860 Hom.: 79488 Cov.: 0 AF XY: 0.569 AC XY: 316986 AN XY: 556834

African (AFR) AF: 0.548 AC: 14538 AN: 26514

American (AMR) AF: 0.556 AC: 19287 AN: 34658

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 11480 AN: 20842

East Asian (EAS) AF: 0.557 AC: 17992 AN: 32286

South Asian (SAS) AF: 0.552 AC: 37095 AN: 67256

European-Finnish (FIN) AF: 0.573 AC: 21051 AN: 36738

Middle Eastern (MID) AF: 0.667 AC: 2989 AN: 4484

European-Non Finnish (NFE) AF: 0.575 AC: 482860 AN: 840410

Other (OTH) AF: 0.566 AC: 26404 AN: 46672

GnomAD4 genome AF: 0.952 AC: 138993 AN: 146074 Hom.: 66214 Cov.: 0 AF XY: 0.953 AC XY: 67547 AN XY: 70878

African (AFR) AF: 0.887 AC: 35531 AN: 40042

American (AMR) AF: 0.972 AC: 14290 AN: 14706

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3369 AN: 3404

East Asian (EAS) AF: 0.992 AC: 4974 AN: 5014

South Asian (SAS) AF: 0.989 AC: 4538 AN: 4588

European-Finnish (FIN) AF: 0.963 AC: 8612 AN: 8942

Middle Eastern (MID) AF: 0.960 AC: 267 AN: 278

European-Non Finnish (NFE) AF: 0.976 AC: 64581 AN: 66174

Other (OTH) AF: 0.959 AC: 1936 AN: 2018

Alfa AF: 0.698 Hom.: 2424

ClinVar

ClinVar submissions as Germline

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.18
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: rs398022187; hg19: chr13-31789169;