rs36692

Positions:

• chr19-17796030-C-T

Variant summary

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

The NM_014256.4(B3GNT3):​c.-51+824C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,988 control chromosomes in the GnomAD database, including 34,502 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 0.66 (34502 hom., cov: 31)
• Consequence: B3GNT3 NM_014256.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

Genes affected

B3GNT3 (HGNC:13528): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GNT3	NM_014256.4	c.-51+824C>T		intron_variant		ENST00000318683.7
B3GNT3	XM_047438042.1	c.-1936C>T		5_prime_UTR_variant	1/3
B3GNT3	XM_011527626.3	c.-51+1147C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GNT3	ENST00000318683.7	c.-51+824C>T		intron_variant		1	NM_014256.4	P1
B3GNT3	ENST00000595387.1	c.-70+824C>T		intron_variant		1		P1
B3GNT3	ENST00000599265.5	c.-51+1147C>T		intron_variant		3
B3GNT3	ENST00000600777.1	c.-51+857C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100256 AN: 151870 Hom.: 34437 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.660 AC: 100386 AN: 151988 Hom.: 34502 Cov.: 31 AF XY: 0.652 AC XY: 48470 AN XY: 74296

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.657

Alfa AF: 0.625 Hom.: 58127

Bravo AF: 0.662

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.37

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: rs36692; hg19: chr19-17906839;