chr17-66262794-A-G

Variant names:

• chr17-66262794-A-G
• rs7208089

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 0.36 in 151,728 control chromosomes in the GnomAD database, including 11,537 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 0.36 (11537 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54526 AN: 151610 Hom.: 11509 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.360 AC: 54602 AN: 151728 Hom.: 11537 Cov.: 30 AF XY: 0.360 AC XY: 26673 AN XY: 74140

African (AFR) AF: 0.581 AC: 23995 AN: 41324

American (AMR) AF: 0.390 AC: 5931 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3464

East Asian (EAS) AF: 0.154 AC: 788 AN: 5132

South Asian (SAS) AF: 0.388 AC: 1863 AN: 4806

European-Finnish (FIN) AF: 0.264 AC: 2779 AN: 10544

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17443 AN: 67922

Other (OTH) AF: 0.321 AC: 679 AN: 2112

Alfa AF: 0.326 Hom.: 1357

Bravo AF: 0.377

Asia WGS AF: 0.323 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7208089; hg19: chr17-64258912;