11-34564065-A-G

Variant names:

• chr11-34564065-A-G
• rs1453390

Variant summary

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

The variant allele was found at a frequency of 0.72 in 152,048 control chromosomes in the GnomAD database, including 39,959 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 0.72 (39959 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109282 AN: 151930 Hom.: 39902 Cov.: 30

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.720 AC: 109401 AN: 152048 Hom.: 39959 Cov.: 30 AF XY: 0.722 AC XY: 53667 AN XY: 74306

African (AFR) AF: 0.785 AC: 32572 AN: 41476

American (AMR) AF: 0.782 AC: 11953 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5120 AN: 5146

South Asian (SAS) AF: 0.818 AC: 3940 AN: 4818

European-Finnish (FIN) AF: 0.635 AC: 6711 AN: 10572

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44442 AN: 67954

Other (OTH) AF: 0.728 AC: 1539 AN: 2114

Alfa AF: 0.726 Hom.: 22836

Bravo AF: 0.734

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.24
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs1453390; hg19: chr11-34585612;