rs9909466

chr17-80525440-G-Cchr17-80525440-G-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 0.179 in 152,162 control chromosomes in the GnomAD database, including 2,619 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 0.18 (2619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.180 AC: 27293 AN: 152044 Hom.: 2619 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.179 AC: 27299 AN: 152162 Hom.: 2619 Cov.: 32 AF XY: 0.174 AC XY: 12942 AN XY: 74390

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0316

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.206

Alfa AF: 0.0938 Hom.: 161

Bravo AF: 0.177

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9909466; hg19: chr17-78499240;