chr11-134432005-C-A

Variant names:

• chr11-134432005-C-A
• rs10791360
• ENST00000533390.7:n.56-4478C>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.56-4478C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 152,112 control chromosomes in the GnomAD database, including 66,441 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 0.93 (66441 hom., cov: 29)
• Consequence: B3GAT1-DT ENST00000533390.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GAT1-DT	ENST00000533390.7	n.56-4478C>A		intron_variant	Intron 1 of 6	1
B3GAT1-DT	ENST00000657630.2	n.62-4478C>A		intron_variant	Intron 1 of 2
B3GAT1-DT	ENST00000661684.2	n.72+19667C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.934 AC: 141977 AN: 151994 Hom.: 66409 Cov.: 29

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.934 AC: 142067 AN: 152112 Hom.: 66441 Cov.: 29 AF XY: 0.933 AC XY: 69382 AN XY: 74350

African (AFR) AF: 0.964 AC: 40018 AN: 41516

American (AMR) AF: 0.946 AC: 14455 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4218 AN: 5146

South Asian (SAS) AF: 0.836 AC: 4003 AN: 4788

European-Finnish (FIN) AF: 0.960 AC: 10177 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62947 AN: 67998

Other (OTH) AF: 0.922 AC: 1943 AN: 2108

Alfa AF: 0.923 Hom.: 33160

Bravo AF: 0.935

Asia WGS AF: 0.841 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10791360; hg19: chr11-134301899;