rs36692

Variant names:

• chr19-17796030-C-T
• rs36692
• NM_014256.4:c.-51+824C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
B3GNT3	NM_014256.4	c.-51+824C>T		intron_variant	Intron 1 of 2	ENST00000318683.7	NP_055071.2
B3GNT3	XM_047438042.1	c.-1936C>T		5_prime_UTR_variant	Exon 1 of 3		XP_047293998.1
B3GNT3	XM_011527626.3	c.-51+1147C>T		intron_variant	Intron 1 of 2		XP_011525928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GNT3	ENST00000318683.7	c.-51+824C>T		intron_variant	Intron 1 of 2	1	NM_014256.4	ENSP00000321874.5
B3GNT3	ENST00000595387.1	c.-70+824C>T		intron_variant	Intron 1 of 2	1		ENSP00000472638.1
B3GNT3	ENST00000599265.5	c.-51+1147C>T		intron_variant	Intron 1 of 2	3		ENSP00000471733.1
B3GNT3	ENST00000600777.1	c.-51+857C>T		intron_variant	Intron 1 of 1	3		ENSP00000468914.1

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

African (AFR) AF: 0.825 AC: 34203 AN: 41450

American (AMR) AF: 0.586 AC: 8944 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5168

South Asian (SAS) AF: 0.449 AC: 2163 AN: 4820

European-Finnish (FIN) AF: 0.643 AC: 6794 AN: 10562

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42809 AN: 67934

Other (OTH) AF: 0.657 AC: 1387 AN: 2112

Alfa AF: 0.639 Hom.: 89466

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
PhyloP100		-2.6
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: rs36692; hg19: chr19-17906839;