rs10791360

chr11-134432005-C-A

Variant summary

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

The ENST00000661684.1(B3GAT1-DT):n.34+19667C>A variant causes a intron, non coding transcript 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 ENST00000661684.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GAT1-DT	ENST00000661684.1	n.34+19667C>A		intron_variant, non_coding_transcript_variant
B3GAT1-DT	ENST00000657630.1	n.56-4478C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.922

Alfa AF: 0.923 Hom.: 29521

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10791360; hg19: chr11-134301899;