Variant 19-17808103-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_014256.4(B3GNT3):c.296C>T(p.Pro99Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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: not found (cov: 31)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

B3GNT3
NM_014256.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.92

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 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.27558404).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GNT3	NM_014256.4 link	c.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 3	ENST00000318683.7	NP_055071.2	Q9Y2A9
B3GNT3	XM_011527626.3 link	c.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 3		XP_011525928.1	Q9Y2A9
B3GNT3	XM_047438042.1 link	c.296C>T	p.Pro99Leu	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.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 3	1	NM_014256.4	ENSP00000321874.5	Q9Y2A9
B3GNT3	ENST00000595387.1 link	c.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 3	1		ENSP00000472638.1	Q9Y2A9
B3GNT3	ENST00000599265.5 link	c.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 3	3		ENSP00000471733.1	M0R199
B3GNT3	ENST00000600777.1 link	c.296C>T	p.Pro99Leu	missense_variant	Exon 2 of 2	3		ENSP00000468914.1	M0QX58

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461668

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.038

T;T;T;T

Eigen

Benign

-0.37

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.32

LIST_S2

Benign

0.64

T;.;T;T

M_CAP

Benign

0.071

MetaRNN

Benign

0.28

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Pathogenic

2.9

.;M;.;M

PrimateAI

Benign

0.45

PROVEAN

Benign

-2.2

.;N;.;.

REVEL

Benign

0.11

Sift

Uncertain

0.0070

.;D;.;.

Sift4G

Uncertain

0.034

D;T;D;T

Polyphen

0.94

.;P;.;P

Vest4

0.26, 0.25

MutPred

0.57

Loss of catalytic residue at P99 (P = 0.0338);Loss of catalytic residue at P99 (P = 0.0338);Loss of catalytic residue at P99 (P = 0.0338);Loss of catalytic residue at P99 (P = 0.0338);

MVP

0.46

MPC

1.0

ClinPred

0.84

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.087

gMVP

0.84

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

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