rs10894818

Positions:

• chr11-134446328-G-A
• chr11-134446328-G-C
• chr11-134446328-G-T

Variant summary

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

The NR_033852.1(B3GAT1-DT):​n.303+9544G>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 0.453 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 NR_033852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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=-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/exons	MANE	UniProt
B3GAT1-DT	NR_033852.1	n.303+9544G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GAT1-DT	ENST00000533390.6	n.50+9544G>A		intron_variant, non_coding_transcript_variant		1
B3GAT1-DT	ENST00000661684.1	n.34+33990G>A		intron_variant, non_coding_transcript_variant
B3GAT1-DT	ENST00000531319.2	n.312+9544G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.498

Alfa AF: 0.472 Hom.: 15801

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10894818; hg19: chr11-134316222;