chr17-66825243-C-A

Variant names:

• chr17-66825243-C-A
• rs873417

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 0.221 in 152,158 control chromosomes in the GnomAD database, including 4,169 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 0.22 (4169 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.221 AC: 33554 AN: 152040 Hom.: 4155 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.221 AC: 33602 AN: 152158 Hom.: 4169 Cov.: 33 AF XY: 0.217 AC XY: 16155 AN XY: 74394

African (AFR) AF: 0.323 AC: 13382 AN: 41484

American (AMR) AF: 0.179 AC: 2735 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.00908 AC: 47 AN: 5178

South Asian (SAS) AF: 0.0576 AC: 278 AN: 4828

European-Finnish (FIN) AF: 0.216 AC: 2288 AN: 10584

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13439 AN: 68000

Other (OTH) AF: 0.196 AC: 414 AN: 2116

Alfa AF: 0.196 Hom.: 5151

Bravo AF: 0.224

Asia WGS AF: 0.0570 AC: 202 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	2.3
DANN	Benign	0.57
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs873417; hg19: chr17-64821361;