19-17811986-G-C

Variant summary

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

The NM_014256.4(B3GNT3):​c.983G>C​(p.Arg328Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R328H) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

B3GNT3
NM_014256.4 missense

Scores

2
17

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]

Genome browser will be placed here

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=0.077699095).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
B3GNT3NM_014256.4 linkc.983G>C p.Arg328Pro missense_variant 3/3 ENST00000318683.7 NP_055071.2 Q9Y2A9
B3GNT3XM_011527626.3 linkc.983G>C p.Arg328Pro missense_variant 3/3 XP_011525928.1 Q9Y2A9
B3GNT3XM_047438042.1 linkc.983G>C p.Arg328Pro missense_variant 3/3 XP_047293998.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
B3GNT3ENST00000318683.7 linkc.983G>C p.Arg328Pro missense_variant 3/31 NM_014256.4 ENSP00000321874.5 Q9Y2A9
B3GNT3ENST00000595387.1 linkc.983G>C p.Arg328Pro missense_variant 3/31 ENSP00000472638.1 Q9Y2A9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
92
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
8.4
DANN
Benign
0.83
DEOGEN2
Benign
0.14
T;T
Eigen
Benign
-0.91
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.18
N
LIST_S2
Benign
0.20
.;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.078
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.2
M;M
PrimateAI
Benign
0.25
T
PROVEAN
Uncertain
-3.0
D;.
REVEL
Benign
0.061
Sift
Benign
0.099
T;.
Sift4G
Benign
0.067
T;T
Polyphen
0.036
B;B
Vest4
0.094
MutPred
0.39
Gain of relative solvent accessibility (P = 0.0275);Gain of relative solvent accessibility (P = 0.0275);
MVP
0.26
MPC
1.4
ClinPred
0.11
T
GERP RS
3.1
Varity_R
0.24
gMVP
0.87

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.

Other links and lift over

dbSNP: rs36686; hg19: chr19-17922795; API