rs1866767

Variant names:

• chr11-134404869-C-T
• rs1866767
• NM_054025.3:c.-282+6938G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_054025.3(B3GAT1):​c.-282+6938G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,190 control chromosomes in the GnomAD database, including 1,763 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 0.14 (1763 hom., cov: 32)
• Consequence: B3GAT1 NM_054025.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• Publications: 5 publications found

Genes affected

B3GAT1 (HGNC:921): (beta-1,3-glucuronyltransferase 1) The protein encoded by this gene is a member of the glucuronyltransferase gene family. These enzymes exhibit strict acceptor specificity, recognizing nonreducing terminal sugars and their anomeric linkages. This gene product functions as the key enzyme in a glucuronyl transfer reaction during the biosynthesis of the carbohydrate epitope HNK-1 (human natural killer-1, also known as CD57 and LEU7). Alternate transcriptional splice variants have been characterized. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GAT1	NM_054025.3	c.-282+6938G>A		intron_variant	Intron 1 of 5	ENST00000312527.9	NP_473366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GAT1	ENST00000312527.9	c.-282+6938G>A		intron_variant	Intron 1 of 5	1	NM_054025.3	ENSP00000307875.4
B3GAT1	ENST00000392580.5	c.-150+6938G>A		intron_variant	Intron 1 of 6	1		ENSP00000376359.1
B3GAT1	ENST00000531510.1	n.174+4839G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21507 AN: 152072 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.142 AC: 21538 AN: 152190 Hom.: 1763 Cov.: 32 AF XY: 0.139 AC XY: 10359 AN XY: 74418

African (AFR) AF: 0.227 AC: 9438 AN: 41488

American (AMR) AF: 0.0856 AC: 1310 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3470

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5170

South Asian (SAS) AF: 0.0879 AC: 424 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8036 AN: 68012

Other (OTH) AF: 0.121 AC: 255 AN: 2114

Alfa AF: 0.124 Hom.: 555

Bravo AF: 0.142

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.89
PhyloP100		-0.92
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: rs1866767; hg19: chr11-134274763;