rs873417

Variant names:

• chr17-66825243-C-A
• rs873417

Your query was ambiguous. Multiple possible variants found:

• chr17-66825243-C-A
• chr17-66825243-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 0.221 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.221 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

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.196

Alfa AF: 0.190 Hom.: 3784

Bravo AF: 0.224

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873417; hg19: chr17-64821361;