rs17165706

Variant names:

• chr7-12208470-A-T
• rs17165706

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 0.273 in 152,084 control chromosomes in the GnomAD database, including 6,689 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 0.27 (6689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.273 AC: 41543 AN: 151966 Hom.: 6684 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.273 AC: 41576 AN: 152084 Hom.: 6689 Cov.: 32 AF XY: 0.272 AC XY: 20202 AN XY: 74342

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.254

Alfa AF: 0.243 Hom.: 653

Bravo AF: 0.273

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17165706; hg19: chr7-12248096;