GeneBe

11-66347477-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_006876.3(B4GAT1):​c.69G>A​(p.Ala23Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000728 in 1,373,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A23A) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

B4GAT1
NM_006876.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.880

Publications

0 publications found
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]
B4GAT1 Gene-Disease associations (from GenCC):
  • muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
  • muscular dystrophy-dystroglycanopathy, type A
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP7
Synonymous conserved (PhyloP=-0.88 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
B4GAT1NM_006876.3 linkc.69G>A p.Ala23Ala synonymous_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.69G>A p.Ala23Ala synonymous_variant Exon 1 of 2 1 NM_006876.3 ENSP00000309096.4 O43505

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.28e-7
AC:
1
AN:
1373468
Hom.:
0
Cov.:
32
AF XY:
0.00000148
AC XY:
1
AN XY:
674388
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30618
American (AMR)
AF:
0.00
AC:
0
AN:
31944
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20718
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38010
South Asian (SAS)
AF:
0.00
AC:
0
AN:
71914
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48564
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5362
European-Non Finnish (NFE)
AF:
9.35e-7
AC:
1
AN:
1069972
Other (OTH)
AF:
0.00
AC:
0
AN:
56366
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
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
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
8.5
DANN
Benign
0.93
PhyloP100
-0.88
PromoterAI
0.072
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6

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

Other links and lift over

dbSNP: rs146812867; hg19: chr11-66114948; API