NM_001159387.2:c.767-957G>A

Variant names:

• chr17-49163131-G-A
• rs4438351
• NM_001159387.2:c.767-957G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001159387.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B4GALNT2	NM_001159387.2	MANE Select	c.767-957G>A		intron	N/A	NP_001152859.1
	B4GALNT2	NM_153446.3		c.947-957G>A		intron	N/A	NP_703147.2
	B4GALNT2	NM_001159388.2		c.689-957G>A		intron	N/A	NP_001152860.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B4GALNT2	ENST00000393354.7	TSL:1 MANE Select	c.767-957G>A		intron	N/A	ENSP00000377022.3
	B4GALNT2	ENST00000300404.2	TSL:1	c.947-957G>A		intron	N/A	ENSP00000300404.2
	B4GALNT2	ENST00000504681.5	TSL:2	c.689-957G>A		intron	N/A	ENSP00000425510.1

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

African (AFR) AF: 0.186 AC: 7686 AN: 41400

American (AMR) AF: 0.237 AC: 3610 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 585 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5146

South Asian (SAS) AF: 0.195 AC: 937 AN: 4814

European-Finnish (FIN) AF: 0.109 AC: 1153 AN: 10552

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11665 AN: 67962

Other (OTH) AF: 0.184 AC: 389 AN: 2110

Alfa AF: 0.184 Hom.: 4573

Bravo AF: 0.202

Asia WGS AF: 0.318 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.78
PhyloP100		-0.39
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: rs4438351; hg19: chr17-47240493;