11-66347509-G-C

Variant summary

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

The NM_006876.3(B4GAT1):​c.37C>G​(p.Gln13Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000739 in 1,353,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.4e-7 ( 0 hom. )

Consequence

B4GAT1
NM_006876.3 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25
Variant links:
Genes affected
B4GAT1 (HGNC:15685): (beta-1,4-glucuronyltransferase 1) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It is essential for the synthesis of poly-N-acetyllactosamine, a determinant for the blood group i antigen. [provided by RefSeq, Jul 2008]

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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=0.11743045).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
B4GAT1NM_006876.3 linkc.37C>G p.Gln13Glu missense_variant Exon 1 of 2 ENST00000311181.5 NP_006867.1 O43505A0A024R5F9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
B4GAT1ENST00000311181.5 linkc.37C>G p.Gln13Glu missense_variant Exon 1 of 2 1 NM_006876.3 ENSP00000309096.4 O43505

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.39e-7
AC:
1
AN:
1353728
Hom.:
0
Cov.:
31
AF XY:
0.00000151
AC XY:
1
AN XY:
662666
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:
9.42e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Uncertain
24
DANN
Benign
0.95
DEOGEN2
Benign
0.14
T
Eigen
Benign
-0.25
Eigen_PC
Benign
-0.048
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.77
T
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-0.90
T
PrimateAI
Uncertain
0.78
T
PROVEAN
Benign
-0.31
N
REVEL
Benign
0.10
Sift
Benign
0.040
D
Sift4G
Benign
0.10
T
Polyphen
0.028
B
Vest4
0.32
MutPred
0.41
Loss of catalytic residue at Q13 (P = 0.0858);
MVP
0.088
MPC
0.94
ClinPred
0.40
T
GERP RS
3.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.22
gMVP
0.52

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-66114980; API