Genetic Variant B4GALT2:c.*622C>T (chr1-43991070-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_003780.5(B4GALT2):c.*622C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 157,512 control chromosomes in the GnomAD database, including 1,920 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 0.13 ( 1892 hom., cov: 32)

Exomes 𝑓: 0.080 ( 28 hom. )

Consequence

B4GALT2
NM_003780.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.62

Publications

14 publications found

Variant links:

Genes affected

B4GALT2 (HGNC:925): (beta-1,4-galactosyltransferase 2) This gene is one of seven beta-1,4-galactosyltransferase (beta4GalT) genes. They encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose; all transfer galactose in a beta1,4 linkage to similar acceptor sugars: GlcNAc, Glc, and Xyl. Each beta4GalT has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus and which then remains uncleaved to function as a transmembrane anchor. By sequence similarity, the beta4GalTs form four groups: beta4GalT1 and beta4GalT2, beta4GalT3 and beta4GalT4, beta4GalT5 and beta4GalT6, and beta4GalT7. The enzyme encoded by this gene synthesizes N-acetyllactosamine in glycolipids and glycoproteins. Its substrate specificity is affected by alpha-lactalbumin but it is not expressed in lactating mammary tissue. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

B4GALT2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B4GALT2	NM_003780.5 link	c.*622C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000372324.6	NP_003771.1	O60909-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B4GALT2	ENST00000372324.6 link	c.*622C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_003780.5	ENSP00000361399.1		O60909-1

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20265

AN:

151956

Hom.:

1888

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0697

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.0951

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.0671

Gnomad OTH

AF:

0.121

GnomAD4 exome

AF:

0.0802

AC:

436

AN:

5438

Hom.:

Cov.:

AF XY:

0.0854

AC XY:

249

AN XY:

2916

show subpopulations

African (AFR)

AF:

0.194

AC:

AN:

American (AMR)

AF:

0.122

AC:

139

AN:

1136

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.0746

AC:

AN:

630

European-Finnish (FIN)

AF:

0.101

AC:

AN:

496

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0588

AC:

166

AN:

2824

Other (OTH)

AF:

0.0691

AC:

AN:

188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.133

AC:

20296

AN:

152074

Hom.:

1892

Cov.:

AF XY:

0.135

AC XY:

10015

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.257

AC:

10630

AN:

41438

American (AMR)

AF:

0.125

AC:

1910

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

242

AN:

3472

East Asian (EAS)

AF:

0.160

AC:

827

AN:

5162

South Asian (SAS)

AF:

0.0956

AC:

460

AN:

4810

European-Finnish (FIN)

AF:

0.125

AC:

1328

AN:

10598

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0671

AC:

4563

AN:

67984

Other (OTH)

AF:

0.119

AC:

252

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

836

1672

2508

3344

4180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.122

Hom.:

330

Bravo

AF:

0.140

Asia WGS

AF:

0.126

AC:

438

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

2.6

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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1-43991070-C-T

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