GeneBe

chr16-67150047-C-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_033309.3(B3GNT9):​c.439G>C​(p.Gly147Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000533 in 1,500,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000030 ( 0 hom. )

Consequence

B3GNT9
NM_033309.3 missense

Scores

3
4
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.79
Variant links:
Genes affected
B3GNT9 (HGNC:28714): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9) Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process. Predicted to be integral component of membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30327776).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
B3GNT9NM_033309.3 linkc.439G>C p.Gly147Arg missense_variant Exon 2 of 2 ENST00000449549.4 NP_171608.2 Q6UX72

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
B3GNT9ENST00000449549.4 linkc.439G>C p.Gly147Arg missense_variant Exon 2 of 2 1 NM_033309.3 ENSP00000400157.3 Q6UX72

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152172
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
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:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000297
AC:
4
AN:
1348664
Hom.:
0
Cov.:
31
AF XY:
0.00000151
AC XY:
1
AN XY:
662632
show subpopulations
African (AFR)
AF:
0.0000705
AC:
2
AN:
28386
American (AMR)
AF:
0.00
AC:
0
AN:
26668
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22114
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34094
South Asian (SAS)
AF:
0.00
AC:
0
AN:
71204
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
45736
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5510
European-Non Finnish (NFE)
AF:
9.44e-7
AC:
1
AN:
1059206
Other (OTH)
AF:
0.0000179
AC:
1
AN:
55746
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152172
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.0000241
AC:
1
AN:
41460
American (AMR)
AF:
0.0000655
AC:
1
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5174
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.0000294
AC:
2
AN:
68010
Other (OTH)
AF:
0.00
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.0000264

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Dec 05, 2024
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.439G>C (p.G147R) alteration is located in exon 2 (coding exon 1) of the B3GNT9 gene. This alteration results from a G to C substitution at nucleotide position 439, causing the glycine (G) at amino acid position 147 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.29
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.15
T
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.76
T
M_CAP
Benign
0.083
D
MetaRNN
Benign
0.30
T
MetaSVM
Benign
-0.75
T
MutationAssessor
Pathogenic
3.0
M
PrimateAI
Pathogenic
0.82
D
PROVEAN
Pathogenic
-5.4
D
REVEL
Benign
0.15
Sift
Benign
0.042
D
Sift4G
Benign
0.061
T
Polyphen
0.54
P
Vest4
0.18
MutPred
0.56
Loss of methylation at R144 (P = 0.0514);
MVP
0.57
MPC
1.1
ClinPred
0.98
D
GERP RS
3.3
Varity_R
0.39
gMVP
0.84
Mutation Taster
=66/34
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs952374866; hg19: chr16-67183950; API