rs34638481

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_194318.4(B3GLCT):c.1105G>A(p.Gly369Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 1,613,940 control chromosomes in the GnomAD database, including 717 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 69 hom., cov: 33)

Exomes 𝑓: 0.027 ( 648 hom. )

Consequence

B3GLCT
NM_194318.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.338

Publications

9 publications found

Variant links:

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)

B3GLCT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016687512).

BP6

Variant 13-31317606-G-A is Benign according to our data. Variant chr13-31317606-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 263091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0232 (3534/152198) while in subpopulation NFE AF = 0.0335 (2281/68014). AF 95% confidence interval is 0.0324. There are 69 homozygotes in GnomAd4. There are 1607 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 69 AR gene

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.1105G>A	p.Gly369Ser	missense	Exon 13 of 15	NP_919299.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.1105G>A	p.Gly369Ser	missense	Exon 13 of 15	ENSP00000343002.4
B3GLCT	ENST00000873566.1		c.916G>A	p.Gly306Ser	missense	Exon 11 of 13	ENSP00000543625.1
B3GLCT	ENST00000946543.1		c.766G>A	p.Gly256Ser	missense	Exon 9 of 11	ENSP00000616602.1

Frequencies

GnomAD3 genomes

AF:

0.0232

AC:

3533

AN:

152080

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00707

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0247

Gnomad ASJ

AF:

0.0605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0154

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0335

Gnomad OTH

AF:

0.0335

GnomAD2 exomes

AF:

0.0252

AC:

6331

AN:

251446

AF XY:

0.0258

show subpopulations

Gnomad AFR exome

AF:

0.00627

Gnomad AMR exome

AF:

0.0199

Gnomad ASJ exome

AF:

0.0607

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0190

Gnomad NFE exome

AF:

0.0331

Gnomad OTH exome

AF:

0.0370

GnomAD4 exome

AF:

0.0266

AC:

38952

AN:

1461742

Hom.:

648

Cov.:

AF XY:

0.0268

AC XY:

19517

AN XY:

727176

show subpopulations

African (AFR)

AF:

0.00591

AC:

198

AN:

33480

American (AMR)

AF:

0.0213

AC:

952

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0587

AC:

1535

AN:

26128

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39698

South Asian (SAS)

AF:

0.0174

AC:

1504

AN:

86258

European-Finnish (FIN)

AF:

0.0216

AC:

1155

AN:

53400

Middle Eastern (MID)

AF:

0.0451

AC:

260

AN:

5768

European-Non Finnish (NFE)

AF:

0.0284

AC:

31555

AN:

1111896

Other (OTH)

AF:

0.0297

AC:

1791

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

2085

4170

6255

8340

10425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1116

2232

3348

4464

5580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0232

AC:

3534

AN:

152198

Hom.:

Cov.:

AF XY:

0.0216

AC XY:

1607

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.00705

AC:

293

AN:

41536

American (AMR)

AF:

0.0247

AC:

377

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0605

AC:

210

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5150

South Asian (SAS)

AF:

0.0156

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.0171

AC:

181

AN:

10614

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0335

AC:

2281

AN:

68014

Other (OTH)

AF:

0.0332

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

173

346

519

692

865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0298

Hom.:

269

Bravo

AF:

0.0226

TwinsUK

AF:

0.0240

AC:

ALSPAC

AF:

0.0280

AC:

108

ESP6500AA

AF:

0.00704

AC:

ESP6500EA

AF:

0.0336

AC:

289

ExAC

AF:

0.0263

AC:

3192

Asia WGS

AF:

0.00808

AC:

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (2)

Peters plus syndrome (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.057

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.53

CADD

Benign

0.0060

(source)

DANN

Benign

0.85

DEOGEN2

Benign

0.026

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.60

MetaRNN

Benign

0.0017

MetaSVM

Benign

-0.86

MutationAssessor

Benign

-1.5

PhyloP100

0.34

PrimateAI

Benign

0.24

PROVEAN

Benign

2.2

REVEL

Benign

0.15

Sift

Benign

1.0

Sift4G

Benign

0.91

Polyphen

0.0

Vest4

0.058

MPC

0.22

ClinPred

0.0019

GERP RS

-3.2

Varity_R

0.021

gMVP

0.25

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over