13-31276666-C-CACAT

Position:

• chr13-31276666-C-CACAT

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_194318.4(B3GLCT):​c.781-34_781-31dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,383,016 control chromosomes in the GnomAD database, including 23,083 homozygotes. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.14 (1908 hom., cov: 29)
  • Exomes 𝑓: 0.18 (21175 hom.)
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.906

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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 13-31276666-C-CACAT is Benign according to our data. Variant chr13-31276666-C-CACAT is described in ClinVar as [Benign]. Clinvar id is 1192419.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GLCT	NM_194318.4	c.781-34_781-31dup		intron_variant		ENST00000343307.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GLCT	ENST00000343307.5	c.781-34_781-31dup		intron_variant		1	NM_194318.4	P1
B3GLCT	ENST00000461652.2	n.396-34_396-31dup		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21168 AN: 151936 Hom.: 1908 Cov.: 29

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.154

GnomAD3 exomes AF: 0.156 AC: 37837 AN: 243054 Hom.: 3465 AF XY: 0.157 AC XY: 20682 AN XY: 132050

Gnomad AFR exome AF: 0.0316

Gnomad AMR exome AF: 0.162

Gnomad ASJ exome AF: 0.137

Gnomad EAS exome AF: 0.000989

Gnomad SAS exome AF: 0.126

Gnomad FIN exome AF: 0.256

Gnomad NFE exome AF: 0.189

Gnomad OTH exome AF: 0.173

GnomAD4 exome AF: 0.176 AC: 216920 AN: 1230962 Hom.: 21175 Cov.: 18 AF XY: 0.175 AC XY: 109026 AN XY: 624640

Gnomad4 AFR exome AF: 0.0309

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.135

Gnomad4 EAS exome AF: 0.000956

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.264

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.139 AC: 21163 AN: 152054 Hom.: 1908 Cov.: 29 AF XY: 0.142 AC XY: 10548 AN XY: 74306

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.152

Alfa AF: 0.170 Hom.: 480

Asia WGS AF: 0.0500 AC: 176 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Peters plus syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		4.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs137981677; hg19: chr13-31850803;