11-134433412-C-G

Variant names:

• chr11-134433412-C-G
• rs7949167
• ENST00000533390.7:n.56-3071C>G

Variant summary

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

The ENST00000533390.7(B3GAT1-DT):​n.56-3071C>G 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 152,324 control chromosomes in the GnomAD database, including 66,528 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 (66528 hom., cov: 34)
• Consequence: B3GAT1-DT ENST00000533390.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• 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=-0.91).
• 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.56-3071C>G		intron_variant	Intron 1 of 6	1
B3GAT1-DT	ENST00000657630.2	n.62-3071C>G		intron_variant	Intron 1 of 2
B3GAT1-DT	ENST00000661684.2	n.72+21074C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142168 AN: 152206 Hom.: 66496 Cov.: 34

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.838

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: 142258 AN: 152324 Hom.: 66528 Cov.: 34 AF XY: 0.933 AC XY: 69500 AN XY: 74482

African (AFR) AF: 0.964 AC: 40068 AN: 41580

American (AMR) AF: 0.946 AC: 14477 AN: 15300

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

East Asian (EAS) AF: 0.821 AC: 4249 AN: 5176

South Asian (SAS) AF: 0.837 AC: 4034 AN: 4818

European-Finnish (FIN) AF: 0.960 AC: 10198 AN: 10624

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

European-Non Finnish (NFE) AF: 0.926 AC: 62978 AN: 68034

Other (OTH) AF: 0.921 AC: 1948 AN: 2114

Alfa AF: 0.935 Hom.: 8275

Bravo AF: 0.935

Asia WGS AF: 0.842 AC: 2928 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	0.80
DANN	Benign	0.52
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7949167; hg19: chr11-134303306;