17-49143364-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001159387.2(B4GALNT2):​c.353+1192C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,110 control chromosomes in the GnomAD database, including 30,232 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 30232 hom., cov: 32)

Consequence

B4GALNT2
NM_001159387.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0530
Variant links:
Genes affected
B4GALNT2 (HGNC:24136): (beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group)) B4GALNT2 catalyzes the last step in the biosynthesis of the human Sd(a) antigen through the addition of an N-acetylgalactosamine residue via a beta-1,4 linkage to a subterminal galactose residue substituted with an alpha-2,3-linked sialic acid. B4GALNT2 also catalyzes the last step in the biosynthesis of the Cad antigen (Montiel et al., 2003 [PubMed 12678917]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
B4GALNT2NM_001159387.2 linkuse as main transcriptc.353+1192C>T intron_variant ENST00000393354.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
B4GALNT2ENST00000393354.7 linkuse as main transcriptc.353+1192C>T intron_variant 1 NM_001159387.2 P1Q8NHY0-2
B4GALNT2ENST00000300404.2 linkuse as main transcriptc.533+1192C>T intron_variant 1 Q8NHY0-1
B4GALNT2ENST00000504681.5 linkuse as main transcriptc.275+1192C>T intron_variant 2 Q8NHY0-3

Frequencies

GnomAD3 genomes
AF:
0.612
AC:
92967
AN:
151992
Hom.:
30164
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.803
Gnomad AMI
AF:
0.553
Gnomad AMR
AF:
0.705
Gnomad ASJ
AF:
0.529
Gnomad EAS
AF:
0.784
Gnomad SAS
AF:
0.643
Gnomad FIN
AF:
0.465
Gnomad MID
AF:
0.617
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.595
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.612
AC:
93096
AN:
152110
Hom.:
30232
Cov.:
32
AF XY:
0.615
AC XY:
45750
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.804
Gnomad4 AMR
AF:
0.706
Gnomad4 ASJ
AF:
0.529
Gnomad4 EAS
AF:
0.784
Gnomad4 SAS
AF:
0.644
Gnomad4 FIN
AF:
0.465
Gnomad4 NFE
AF:
0.487
Gnomad4 OTH
AF:
0.599
Alfa
AF:
0.514
Hom.:
20065
Bravo
AF:
0.642
Asia WGS
AF:
0.728
AC:
2528
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
2.0
DANN
Benign
0.42

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: rs9902755; hg19: chr17-47220726; API