rs9460309

Variant names:

• chr6-19220421-A-G
• rs9460309

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 0.314 in 151,960 control chromosomes in the GnomAD database, including 8,658 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 0.31 (8658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.313 AC: 47599 AN: 151842 Hom.: 8621 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.314 AC: 47692 AN: 151960 Hom.: 8658 Cov.: 32 AF XY: 0.316 AC XY: 23491 AN XY: 74274

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.333

Alfa AF: 0.246 Hom.: 2277

Bravo AF: 0.342

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9460309; hg19: chr6-19220652;