rs7928758

Positions:

• chr11-134396073-T-G

Variant summary

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

The NM_054025.3(B3GAT1):​c.-281-8133A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,110 control chromosomes in the GnomAD database, including 2,117 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 0.16 (2117 hom., cov: 33)
• Consequence: B3GAT1 NM_054025.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GAT1	NM_054025.3	c.-281-8133A>C		intron_variant		ENST00000312527.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GAT1	ENST00000312527.9	c.-281-8133A>C		intron_variant		1	NM_054025.3	P1
B3GAT1	ENST00000392580.5	c.-149-8133A>C		intron_variant		1		P1
B3GAT1	ENST00000531510.1	n.175-8133A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24168 AN: 151992 Hom.: 2107 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.159 AC: 24205 AN: 152110 Hom.: 2117 Cov.: 33 AF XY: 0.157 AC XY: 11686 AN XY: 74350

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.136

Alfa AF: 0.148 Hom.: 2549

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.49

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: rs7928758; hg19: chr11-134265967;