rs9460309

Variant names:

• chr6-19220421-A-G
• rs9460309

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.473 AC: 19576 AN: 41402

American (AMR) AF: 0.428 AC: 6539 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1446 AN: 5144

South Asian (SAS) AF: 0.375 AC: 1803 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10564

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14574 AN: 67978

Other (OTH) AF: 0.333 AC: 703 AN: 2114

Alfa AF: 0.255 Hom.: 3330

Bravo AF: 0.342

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs9460309; hg19: chr6-19220652;