11-66347429-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006876.3(B4GAT1):c.117G>A(p.Gln39Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 1,573,756 control chromosomes in the GnomAD database, including 7,658 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1486 hom., cov: 32)

Exomes 𝑓: 0.088 ( 6172 hom. )

Consequence

B4GAT1
NM_006876.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.16

Publications

26 publications found

Variant links:

Genes affected

B4GAT1 (HGNC:15685): (beta-1,4-glucuronyltransferase 1) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It is essential for the synthesis of poly-N-acetyllactosamine, a determinant for the blood group i antigen. [provided by RefSeq, Jul 2008]

B4GAT1 Gene-Disease associations (from GenCC):

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
muscular dystrophy-dystroglycanopathy, type A
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

B4GAT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 11-66347429-C-T is Benign according to our data. Variant chr11-66347429-C-T is described in ClinVar as Benign. ClinVar VariationId is 260057.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B4GAT1	NM_006876.3 link	c.117G>A	p.Gln39Gln	synonymous_variant	Exon 1 of 2	ENST00000311181.5	NP_006867.1	O43505A0A024R5F9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B4GAT1	ENST00000311181.5 link	c.117G>A	p.Gln39Gln	synonymous_variant	Exon 1 of 2	1	NM_006876.3	ENSP00000309096.4		O43505

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18650

AN:

152138

Hom.:

1486

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.0429

Gnomad AMR

AF:

0.0862

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.0492

Gnomad FIN

AF:

0.0474

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0829

Gnomad OTH

AF:

0.115

GnomAD2 exomes

AF:

0.0956

AC:

19153

AN:

200426

AF XY:

0.0928

show subpopulations

Gnomad AFR exome

AF:

0.237

Gnomad AMR exome

AF:

0.0543

Gnomad ASJ exome

AF:

0.111

Gnomad EAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.0536

Gnomad NFE exome

AF:

0.0892

Gnomad OTH exome

AF:

0.0873

GnomAD4 exome

AF:

0.0875

AC:

124447

AN:

1421500

Hom.:

6172

Cov.:

AF XY:

0.0862

AC XY:

60645

AN XY:

703164

show subpopulations

African (AFR)

AF:

0.234

AC:

7617

AN:

32524

American (AMR)

AF:

0.0583

AC:

2315

AN:

39686

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

2436

AN:

23940

East Asian (EAS)

AF:

0.167

AC:

6477

AN:

38704

South Asian (SAS)

AF:

0.0543

AC:

4333

AN:

79834

European-Finnish (FIN)

AF:

0.0553

AC:

2790

AN:

50460

Middle Eastern (MID)

AF:

0.115

AC:

647

AN:

5624

European-Non Finnish (NFE)

AF:

0.0844

AC:

92218

AN:

1092128

Other (OTH)

AF:

0.0958

AC:

5614

AN:

58600

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

6638

13276

19914

26552

33190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3620

7240

10860

14480

18100

<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:

0.123

AC:

18673

AN:

152256

Hom.:

1486

Cov.:

AF XY:

0.119

AC XY:

8849

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.227

AC:

9424

AN:

41544

American (AMR)

AF:

0.0861

AC:

1317

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

359

AN:

3472

East Asian (EAS)

AF:

0.169

AC:

873

AN:

5170

South Asian (SAS)

AF:

0.0501

AC:

242

AN:

4832

European-Finnish (FIN)

AF:

0.0474

AC:

503

AN:

10616

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0829

AC:

5639

AN:

68010

Other (OTH)

AF:

0.113

AC:

239

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

819

1639

2458

3278

4097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.103

Hom.:

1186

Bravo

AF:

0.132

Asia WGS

AF:

0.105

AC:

364

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 20, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

9.6

(source)

DANN

Benign

0.94

PhyloP100

1.2

PromoterAI

-0.031

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over