rs17165706

chr7-12208470-A-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 0.273 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;