rs4438351

chr17-49163131-G-Achr17-49163131-G-Cchr17-49163131-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001159387.2(B4GALNT2):c.767-957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,904 control chromosomes in the GnomAD database, including 3,179 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 0.19 (3179 hom., cov: 30)
• Consequence: B4GALNT2 NM_001159387.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B4GALNT2	NM_001159387.2	c.767-957G>A		intron_variant		ENST00000393354.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B4GALNT2	ENST00000393354.7	c.767-957G>A		intron_variant		1	NM_001159387.2	P1
B4GALNT2	ENST00000300404.2	c.947-957G>A		intron_variant		1
B4GALNT2	ENST00000504681.5	c.689-957G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28872 AN: 151786 Hom.: 3169 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.182

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28897 AN: 151904 Hom.: 3179 Cov.: 30 AF XY: 0.192 AC XY: 14245 AN XY: 74242

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.184

Alfa AF: 0.183 Hom.: 3140

Bravo AF: 0.202

Asia WGS AF: 0.318 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.30
Dann	Benign	0.78

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

Other links and lift over

dbSNP: rs4438351; hg19: chr17-47240493;