dbSNP rs9542307: B3GLCT:c.347+20C>G (chr13-31247119-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_194318.4(B3GLCT):c.347+20C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 1,576,512 control chromosomes in the GnomAD database, including 148,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11669 hom., cov: 30)

Exomes 𝑓: 0.43 ( 137228 hom. )

Consequence

B3GLCT
NM_194318.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -1.31

Publications

12 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: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Orphanet

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 (BayesDel_noAF=-0.91).

BP6

Variant 13-31247119-C-G is Benign according to our data. Variant chr13-31247119-C-G is described in ClinVar as Benign. ClinVar VariationId is 96626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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.347+20C>G		intron	N/A	NP_919299.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.347+20C>G	intron	N/A	ENSP00000343002.4	Q6Y288
B3GLCT	ENST00000873566.1		c.271-13827C>G	intron	N/A	ENSP00000543625.1
B3GLCT	ENST00000946543.1		c.121-13827C>G	intron	N/A	ENSP00000616602.1

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57164

AN:

151748

Hom.:

11671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.0660

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.374

GnomAD2 exomes

AF:

0.359

AC:

89890

AN:

250636

AF XY:

0.362

show subpopulations

Gnomad AFR exome

AF:

0.279

Gnomad AMR exome

AF:

0.273

Gnomad ASJ exome

AF:

0.365

Gnomad EAS exome

AF:

0.0545

Gnomad FIN exome

AF:

0.405

Gnomad NFE exome

AF:

0.469

Gnomad OTH exome

AF:

0.392

GnomAD4 exome

AF:

0.429

AC:

610683

AN:

1424646

Hom.:

137228

Cov.:

AF XY:

0.424

AC XY:

301352

AN XY:

711084

show subpopulations

African (AFR)

AF:

0.274

AC:

8877

AN:

32440

American (AMR)

AF:

0.278

AC:

12409

AN:

44620

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

9276

AN:

25848

East Asian (EAS)

AF:

0.0448

AC:

1765

AN:

39380

South Asian (SAS)

AF:

0.238

AC:

20287

AN:

85244

European-Finnish (FIN)

AF:

0.408

AC:

21769

AN:

53312

Middle Eastern (MID)

AF:

0.371

AC:

2110

AN:

5692

European-Non Finnish (NFE)

AF:

0.473

AC:

510546

AN:

1079064

Other (OTH)

AF:

0.400

AC:

23644

AN:

59046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

15872

31745

47617

63490

79362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14594

29188

43782

58376

72970

<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:

0.376

AC:

57172

AN:

151866

Hom.:

11669

Cov.:

AF XY:

0.369

AC XY:

27346

AN XY:

74190

show subpopulations

African (AFR)

AF:

0.276

AC:

11440

AN:

41436

American (AMR)

AF:

0.344

AC:

5250

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

1209

AN:

3464

East Asian (EAS)

AF:

0.0654

AC:

338

AN:

5168

South Asian (SAS)

AF:

0.222

AC:

1066

AN:

4802

European-Finnish (FIN)

AF:

0.408

AC:

4282

AN:

10494

Middle Eastern (MID)

AF:

0.414

AC:

121

AN:

292

European-Non Finnish (NFE)

AF:

0.473

AC:

32115

AN:

67926

Other (OTH)

AF:

0.374

AC:

790

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1703

3406

5110

6813

8516

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

544

1088

1632

2176

2720

<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:

0.344

Hom.:

1553

Bravo

AF:

0.369

Asia WGS

AF:

0.172

AC:

600

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

not provided (2)

Peters plus syndrome (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

DANN

Benign

0.54

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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