17-11040069-C-T

Variant names:

• chr17-11040069-C-T
• rs1468482

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 0.775 in 151,664 control chromosomes in the GnomAD database, including 47,435 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 0.77 (47435 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117479 AN: 151546 Hom.: 47424 Cov.: 28

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.775 AC: 117513 AN: 151664 Hom.: 47435 Cov.: 28 AF XY: 0.777 AC XY: 57569 AN XY: 74122

African (AFR) AF: 0.519 AC: 21391 AN: 41214

American (AMR) AF: 0.847 AC: 12901 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4932 AN: 5128

South Asian (SAS) AF: 0.843 AC: 4029 AN: 4782

European-Finnish (FIN) AF: 0.857 AC: 9039 AN: 10550

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59551 AN: 67976

Other (OTH) AF: 0.786 AC: 1653 AN: 2102

Alfa AF: 0.845 Hom.: 28106

Bravo AF: 0.764

Asia WGS AF: 0.875 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.37
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1468482; hg19: chr17-10943386;