13-31317424-T-C

Variant names:

• chr13-31317424-T-C
• rs1041074
• NM_194318.4:c.1065-142T>C

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.1065-142T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.996 in 152,334 control chromosomes in the GnomAD database, including 75,618 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 1.0 (75618 hom., cov: 33)
  • Exomes 𝑓: 1.0 (399586 hom.)
  • Failed GnomAD Quality Control
• Consequence: B3GLCT NM_194318.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.37
• 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: 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=-0.92).
• BP6: Variant 13-31317424-T-C is Benign according to our data. Variant chr13-31317424-T-C is described in ClinVar as Benign. ClinVar VariationId is 1282985.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.1065-142T>C		intron_variant	Intron 12 of 14	ENST00000343307.5	NP_919299.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.1065-142T>C		intron_variant	Intron 12 of 14	1	NM_194318.4	ENSP00000343002.4

Frequencies

GnomAD3 genomes AF: 0.996 AC: 151670 AN: 152216 Hom.: 75564 Cov.: 33

Gnomad AFR AF: 0.988

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.998

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.998

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.997

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 1.00 AC: 799535 AN: 799902 Hom.: 399586 AF XY: 1.00 AC XY: 420018 AN XY: 420168

African (AFR) AF: 0.989 AC: 20136 AN: 20364

American (AMR) AF: 0.999 AC: 39413 AN: 39448

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 20556 AN: 20556

East Asian (EAS) AF: 1.00 AC: 34868 AN: 34868

South Asian (SAS) AF: 1.00 AC: 68842 AN: 68844

European-Finnish (FIN) AF: 0.998 AC: 38579 AN: 38646

Middle Eastern (MID) AF: 0.999 AC: 4332 AN: 4336

European-Non Finnish (NFE) AF: 1.00 AC: 534987 AN: 534996

Other (OTH) AF: 0.999 AC: 37822 AN: 37844

GnomAD4 genome AF: 0.996 AC: 151783 AN: 152334 Hom.: 75618 Cov.: 33 AF XY: 0.996 AC XY: 74224 AN XY: 74494

African (AFR) AF: 0.988 AC: 41079 AN: 41568

American (AMR) AF: 0.998 AC: 15273 AN: 15302

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 1.00 AC: 4826 AN: 4826

European-Finnish (FIN) AF: 0.998 AC: 10597 AN: 10620

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68038 AN: 68042

Other (OTH) AF: 0.997 AC: 2108 AN: 2114

Alfa AF: 0.998 Hom.: 9258

Bravo AF: 0.996

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jul 05, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		-1.4
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: rs1041074; hg19: chr13-31891561;