rs11652805

chr17-64991033-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.666

Alfa AF: 0.793 Hom.: 105613

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11652805; hg19: chr17-62987151;