rs1045721

chr11-134379712-G-A

Variant summary

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

The NM_054025.3(B3GAT1):c.*1050C>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 0.0911 in 152,328 control chromosomes in the GnomAD database, including 914 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 0.091 (913 hom., cov: 33)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: B3GAT1 NM_054025.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GAT1	NM_054025.3	c.*1050C>T		3_prime_UTR_variant	6/6	ENST00000312527.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GAT1	ENST00000312527.9	c.*1050C>T		3_prime_UTR_variant	6/6	1	NM_054025.3	P1
B3GAT1	ENST00000392580.5	c.*1050C>T		3_prime_UTR_variant	7/7	1		P1
B3GAT1	ENST00000531778.1	n.4952C>T		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13839 AN: 152002 Hom.: 911 Cov.: 33

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0995

GnomAD4 exome AF: 0.139 AC: 29 AN: 208 Hom.: 1 Cov.: 0 AF XY: 0.120 AC XY: 19 AN XY: 158

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.0910 AC: 13850 AN: 152120 Hom.: 913 Cov.: 33 AF XY: 0.0919 AC XY: 6833 AN XY: 74352

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0990

Alfa AF: 0.118 Hom.: 1408

Bravo AF: 0.0824

Asia WGS AF: 0.0240 AC: 83 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	0.99
Dann	Benign	0.61

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: rs1045721; hg19: chr11-134249606;