13-31276666-C-CACAT

Variant names:

• chr13-31276666-C-CACAT
• rs137981677
• NM_194318.4:c.781-34_781-31dupCATA

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.781-34_781-31dupCATA 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.781-34_781-31dupCATA		intron_variant	Intron 9 of 14	ENST00000343307.5	NP_919299.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.781-36_781-35insACAT		intron_variant	Intron 9 of 14	1	NM_194318.4	ENSP00000343002.4
B3GLCT	ENST00000461652.2	n.396-36_396-35insACAT		intron_variant	Intron 4 of 6	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

GnomAD2 exomes AF: 0.156 AC: 37837 AN: 243054 AF XY: 0.157

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 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 AC: 901 AN: 29150

Gnomad4 AMR exome AF: 0.162 AC: 7194 AN: 44326

Gnomad4 ASJ exome AF: 0.135 AC: 3327 AN: 24680

Gnomad4 EAS exome AF: 0.000956 AC: 37 AN: 38690

Gnomad4 SAS exome AF: 0.128 AC: 10444 AN: 81590

Gnomad4 FIN exome AF: 0.264 AC: 13222 AN: 50090

Gnomad4 NFE exome AF: 0.190 AC: 172168 AN: 904360

Gnomad4 Remaining exome AF: 0.165 AC: 8708 AN: 52760

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 AC: 0.0341314 AN: 0.0341314

Gnomad4 AMR AF: 0.166 AC: 0.165684 AN: 0.165684

Gnomad4 ASJ AF: 0.141 AC: 0.140841 AN: 0.140841

Gnomad4 EAS AF: 0.00212 AC: 0.00212028 AN: 0.00212028

Gnomad4 SAS AF: 0.118 AC: 0.117928 AN: 0.117928

Gnomad4 FIN AF: 0.268 AC: 0.267579 AN: 0.267579

Gnomad4 NFE AF: 0.190 AC: 0.190068 AN: 0.190068

Gnomad4 OTH AF: 0.152 AC: 0.152174 AN: 0.152174

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

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Jul 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		4.0
Mutation Taster		=100/0	polymorphism (auto)

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;