chr17-49143364-C-T

Variant names:

• chr17-49143364-C-T
• rs9902755
• NM_001159387.2:c.353+1192C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
B4GALNT2	NM_001159387.2	c.353+1192C>T		intron_variant	Intron 3 of 10	ENST00000393354.7	NP_001152859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B4GALNT2	ENST00000393354.7	c.353+1192C>T		intron_variant	Intron 3 of 10	1	NM_001159387.2	ENSP00000377022.3
B4GALNT2	ENST00000300404.2	c.533+1192C>T		intron_variant	Intron 3 of 10	1		ENSP00000300404.2
B4GALNT2	ENST00000504681.5	c.275+1192C>T		intron_variant	Intron 3 of 10	2		ENSP00000425510.1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92967 AN: 151992 Hom.: 30164 Cov.: 32

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

African (AFR) AF: 0.804 AC: 33350 AN: 41500

American (AMR) AF: 0.706 AC: 10789 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1837 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4062 AN: 5182

South Asian (SAS) AF: 0.644 AC: 3106 AN: 4824

European-Finnish (FIN) AF: 0.465 AC: 4910 AN: 10548

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33096 AN: 67990

Other (OTH) AF: 0.599 AC: 1264 AN: 2110

Alfa AF: 0.542 Hom.: 68564

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
PhyloP100		-0.053
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9902755; hg19: chr17-47220726;