Genetic Variant B3GAT1:c.-281-308T>G (chr11-134388248-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_054025.3(B3GAT1):c.-281-308T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 238,104 control chromosomes in the GnomAD database, including 777 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.052 ( 702 hom., cov: 33)

Exomes 𝑓: 0.010 ( 75 hom. )

Consequence

B3GAT1
NM_054025.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

1 publications found

Variant links:

Genes affected

B3GAT1 (HGNC:921): (beta-1,3-glucuronyltransferase 1) The protein encoded by this gene is a member of the glucuronyltransferase gene family. These enzymes exhibit strict acceptor specificity, recognizing nonreducing terminal sugars and their anomeric linkages. This gene product functions as the key enzyme in a glucuronyl transfer reaction during the biosynthesis of the carbohydrate epitope HNK-1 (human natural killer-1, also known as CD57 and LEU7). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

B3GAT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054025.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
B3GAT1	NM_054025.3	MANE Select	c.-281-308T>G	intron	N/A	NP_473366.1
B3GAT1	NM_001367973.1		c.-93-308T>G	intron	N/A	NP_001354902.1
B3GAT1	NM_018644.3		c.-149-308T>G	intron	N/A	NP_061114.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
B3GAT1	ENST00000312527.9	TSL:1 MANE Select	c.-281-308T>G	intron	N/A	ENSP00000307875.4
B3GAT1	ENST00000392580.5	TSL:1	c.-149-308T>G	intron	N/A	ENSP00000376359.1
B3GAT1	ENST00000524765.1	TSL:2	c.-440T>G	5_prime_UTR	Exon 1 of 6	ENSP00000433847.1

Frequencies

GnomAD3 genomes

AF:

0.0524

AC:

7970

AN:

152086

Hom.:

700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0230

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000808

Gnomad OTH

AF:

0.0334

GnomAD4 exome

AF:

0.0103

AC:

883

AN:

85900

Hom.:

Cov.:

AF XY:

0.00886

AC XY:

394

AN XY:

44486

show subpopulations

African (AFR)

AF:

0.178

AC:

758

AN:

4252

American (AMR)

AF:

0.0105

AC:

AN:

6404

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2150

East Asian (EAS)

AF:

0.00

AC:

AN:

6646

South Asian (SAS)

AF:

0.000708

AC:

AN:

11302

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2600

Middle Eastern (MID)

AF:

0.00318

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.000293

AC:

AN:

47738

Other (OTH)

AF:

0.00779

AC:

AN:

4494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

104

139

174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.0525

AC:

7988

AN:

152204

Hom.:

702

Cov.:

AF XY:

0.0516

AC XY:

3843

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.181

AC:

7503

AN:

41494

American (AMR)

AF:

0.0230

AC:

352

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5156

South Asian (SAS)

AF:

0.000830

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000808

AC:

AN:

68028

Other (OTH)

AF:

0.0331

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

333

666

998

1331

1664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0346

Hom.:

Bravo

AF:

0.0601

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.9

(source)

DANN

Benign

0.60

PhyloP100

0.064

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