rs9458005

chr6-160697545-A-G

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 0.207 in 151,950 control chromosomes in the GnomAD database, including 3,226 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 0.21 (3226 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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: 0.207 AC: 31384 AN: 151832 Hom.: 3209 Cov.: 30

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.207 AC: 31436 AN: 151950 Hom.: 3226 Cov.: 30 AF XY: 0.206 AC XY: 15333 AN XY: 74274

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.198

Alfa AF: 0.214 Hom.: 4591

Bravo AF: 0.202

Asia WGS AF: 0.202 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.54
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9458005; hg19: chr6-161118577;