Genetic Variant NM_054025.3: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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GAT1	NM_054025.3 link	c.-281-308T>G		intron_variant	Intron 1 of 5	ENST00000312527.9	NP_473366.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
B3GAT1	ENST00000312527.9 link	c.-281-308T>G	intron_variant	Intron 1 of 5	1	NM_054025.3	ENSP00000307875.4
B3GAT1	ENST00000392580.5 link	c.-149-308T>G	intron_variant	Intron 1 of 6	1		ENSP00000376359.1
B3GAT1	ENST00000524765.1 link	c.-440T>G	5_prime_UTR_variant	Exon 1 of 6	2		ENSP00000433847.1
B3GAT1	ENST00000531510.1 link	n.175-308T>G	intron_variant	Intron 1 of 2	3

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over