Variant 19-17811986-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014256.4(B3GNT3):c.983G>A(p.Arg328His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,603,612 control chromosomes in the GnomAD database, including 468,645 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.79 ( 48333 hom., cov: 32)

Exomes 𝑓: 0.76 ( 420312 hom. )

Consequence

B3GNT3
NM_014256.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360

Variant links:

Genes affected

B3GNT3 (HGNC:13528): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]

B3GNT3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.214042E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
B3GNT3	NM_014256.4 linkuse as main transcript	c.983G>A	p.Arg328His	missense_variant	3/3	ENST00000318683.7	NP_055071.2
B3GNT3	XM_011527626.3 linkuse as main transcript	c.983G>A	p.Arg328His	missense_variant	3/3		XP_011525928.1
B3GNT3	XM_047438042.1 linkuse as main transcript	c.983G>A	p.Arg328His	missense_variant	3/3		XP_047293998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GNT3	ENST00000318683.7 linkuse as main transcript	c.983G>A	p.Arg328His	missense_variant	3/3	1	NM_014256.4	ENSP00000321874	P1
B3GNT3	ENST00000595387.1 linkuse as main transcript	c.983G>A	p.Arg328His	missense_variant	3/3	1		ENSP00000472638	P1

Frequencies

GnomAD3 genomes

AF:

0.793

AC:

120579

AN:

152104

Hom.:

48294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.878

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.802

Gnomad ASJ

AF:

0.782

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.711

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.774

GnomAD3 exomes

AF:

0.761

AC:

185707

AN:

244150

Hom.:

71610

AF XY:

0.757

AC XY:

100340

AN XY:

132538

show subpopulations

Gnomad AFR exome

AF:

0.885

Gnomad AMR exome

AF:

0.807

Gnomad ASJ exome

AF:

0.786

Gnomad EAS exome

AF:

0.486

Gnomad SAS exome

AF:

0.735

Gnomad FIN exome

AF:

0.839

Gnomad NFE exome

AF:

0.767

Gnomad OTH exome

AF:

0.762

GnomAD4 exome

AF:

0.759

AC:

1101909

AN:

1451390

Hom.:

420312

Cov.:

AF XY:

0.758

AC XY:

547377

AN XY:

722418

show subpopulations

Gnomad4 AFR exome

AF:

0.885

Gnomad4 AMR exome

AF:

0.805

Gnomad4 ASJ exome

AF:

0.784

Gnomad4 EAS exome

AF:

0.520

Gnomad4 SAS exome

AF:

0.737

Gnomad4 FIN exome

AF:

0.835

Gnomad4 NFE exome

AF:

0.760

Gnomad4 OTH exome

AF:

0.764

GnomAD4 genome

AF:

0.793

AC:

120673

AN:

152222

Hom.:

48333

Cov.:

AF XY:

0.794

AC XY:

59089

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.877

Gnomad4 AMR

AF:

0.803

Gnomad4 ASJ

AF:

0.782

Gnomad4 EAS

AF:

0.509

Gnomad4 SAS

AF:

0.712

Gnomad4 FIN

AF:

0.840

Gnomad4 NFE

AF:

0.763

Gnomad4 OTH

AF:

0.768

Alfa

AF:

0.760

Hom.:

100817

Bravo

AF:

0.791

TwinsUK

AF:

0.774

AC:

2869

ALSPAC

AF:

0.763

AC:

2939

ESP6500AA

AF:

0.877

AC:

3865

ESP6500EA

AF:

0.755

AC:

6493

ExAC

AF:

0.763

AC:

92625

Asia WGS

AF:

0.648

AC:

2255

AN:

3478

EpiCase

AF:

0.754

EpiControl

AF:

0.760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.8

DANN

Benign

0.96

DEOGEN2

Benign

0.064

T;T

Eigen

Benign

-0.78

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.24

.;T

MetaRNN

Benign

0.0000012

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.6

L;L

MutationTaster

Benign

1.0

PrimateAI

Benign

0.23

PROVEAN

Benign

-2.0

N;.

REVEL

Benign

0.024

Sift

Benign

0.26

T;.

Sift4G

Uncertain

0.017

D;D

Polyphen

0.45

B;B

Vest4

0.020

MPC

0.85

ClinPred

0.0024

GERP RS

3.1

Varity_R

0.032

gMVP

0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over