ENST00000533390.7:n.357+9544G>A

Variant names:

• chr11-134446328-G-A
• rs10894818
• ENST00000533390.7:n.357+9544G>A

Variant summary

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

The ENST00000533390.7(B3GAT1-DT):​n.357+9544G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,880 control chromosomes in the GnomAD database, including 16,172 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 0.45 (16172 hom., cov: 32)
• Consequence: B3GAT1-DT ENST00000533390.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 6 publications found

Genes affected

B3GAT1-DT (HGNC:27449): (B3GAT1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GAT1-DT	NR_033852.1	n.303+9544G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GAT1-DT	ENST00000533390.7	n.357+9544G>A		intron_variant	Intron 2 of 6	1
B3GAT1-DT	ENST00000531319.2	n.312+9544G>A		intron_variant	Intron 1 of 4	2
B3GAT1-DT	ENST00000661684.2	n.72+33990G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68753 AN: 151762 Hom.: 16155 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.453 AC: 68804 AN: 151880 Hom.: 16172 Cov.: 32 AF XY: 0.460 AC XY: 34178 AN XY: 74222

African (AFR) AF: 0.319 AC: 13202 AN: 41402

American (AMR) AF: 0.582 AC: 8886 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1728 AN: 3464

East Asian (EAS) AF: 0.503 AC: 2561 AN: 5094

South Asian (SAS) AF: 0.503 AC: 2410 AN: 4794

European-Finnish (FIN) AF: 0.536 AC: 5674 AN: 10586

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32804 AN: 67952

Other (OTH) AF: 0.498 AC: 1046 AN: 2102

Alfa AF: 0.471 Hom.: 21037

Bravo AF: 0.452

Asia WGS AF: 0.512 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.42
PhyloP100		-0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10894818; hg19: chr11-134316222;