Genetic Variant NM_014256.4:c.179C>G (chr19-17807986-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014256.4(B3GNT3):c.179C>G(p.Pro60Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 27)

Consequence

B3GNT3
NM_014256.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.072110355).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GNT3	NM_014256.4 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3	ENST00000318683.7	NP_055071.2	Q9Y2A9
B3GNT3	XM_011527626.3 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3		XP_011525928.1	Q9Y2A9
B3GNT3	XM_047438042.1 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3		XP_047293998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
B3GNT3	ENST00000318683.7 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3	1	NM_014256.4	ENSP00000321874.5	Q9Y2A9
B3GNT3	ENST00000595387.1 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3	1		ENSP00000472638.1	Q9Y2A9
B3GNT3	ENST00000599265.5 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 3	3		ENSP00000471733.1	M0R199
B3GNT3	ENST00000600777.1 link	c.179C>G	p.Pro60Arg	missense_variant	Exon 2 of 2	3		ENSP00000468914.1	M0QX58

Frequencies

GnomAD3 genomes

AF:

0.0000132

AC:

AN:

151278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000295

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000409

AC:

AN:

244480

Hom.:

AF XY:

0.00

AC XY:

AN XY:

132810

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000914

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.0000132

AC:

AN:

151278

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

73878

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000295

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.00000378

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

0.46

DANN

Benign

0.76

DEOGEN2

Benign

0.013

T;T;T;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.071

LIST_S2

Benign

0.34

T;.;T;T

M_CAP

Benign

0.040

MetaRNN

Benign

0.072

T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.2

.;L;.;L

PrimateAI

Benign

0.38

PROVEAN

Uncertain

-2.4

.;N;.;.

REVEL

Benign

0.016

Sift

Benign

0.53

.;T;.;.

Sift4G

Benign

0.30

T;T;T;T

Polyphen

0.0030

.;B;.;B

Vest4

0.12, 0.12

MutPred

0.24

Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);

MVP

0.16

MPC

0.74

ClinPred

0.020

GERP RS

-2.0

Varity_R

0.039

gMVP

0.29

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