chr17-49174686-G-T

Position:

• chr17-49174686-G-T

Variant summary

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

The ENST00000393354.7(B4GALNT2):​c.*4958G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,012 control chromosomes in the GnomAD database, including 10,317 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 0.36 (10317 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: B4GALNT2 ENST00000393354.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B4GALNT2	NM_001159387.2	c.*4958G>T		3_prime_UTR_variant	11/11	ENST00000393354.7	NP_001152859.1
B4GALNT2	NM_001159388.2	c.*4958G>T		3_prime_UTR_variant	11/11		NP_001152860.1
B4GALNT2	NM_153446.3	c.*4958G>T		3_prime_UTR_variant	11/11		NP_703147.2
B4GALNT2	XM_017024173.2	c.*4958G>T		3_prime_UTR_variant	11/11		XP_016879662.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B4GALNT2	ENST00000393354.7	c.*4958G>T		3_prime_UTR_variant	11/11	1	NM_001159387.2	ENSP00000377022	P1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55470 AN: 151894 Hom.: 10318 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.368

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.365 AC: 55472 AN: 152012 Hom.: 10317 Cov.: 32 AF XY: 0.363 AC XY: 26955 AN XY: 74316

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.369

Alfa AF: 0.370 Hom.: 1323

Bravo AF: 0.373

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7222737; hg19: chr17-47252048;