rs11652805

Variant names:

• chr17-64991033-C-T
• rs11652805

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 0.633 in 152,100 control chromosomes in the GnomAD database, including 36,830 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 0.63 (36830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96331 AN: 151982 Hom.: 36821 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.633 AC: 96342 AN: 152100 Hom.: 36830 Cov.: 32 AF XY: 0.639 AC XY: 47493 AN XY: 74376

African (AFR) AF: 0.173 AC: 7184 AN: 41472

American (AMR) AF: 0.750 AC: 11466 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3470

East Asian (EAS) AF: 0.759 AC: 3911 AN: 5156

South Asian (SAS) AF: 0.785 AC: 3785 AN: 4820

European-Finnish (FIN) AF: 0.839 AC: 8879 AN: 10582

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55968 AN: 67996

Other (OTH) AF: 0.666 AC: 1407 AN: 2114

Alfa AF: 0.757 Hom.: 149890

Bravo AF: 0.603

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11652805; hg19: chr17-62987151;