rs9320815

Variant names:

• chr6-121411344-A-G
• rs9320815

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 0.204 in 152,090 control chromosomes in the GnomAD database, including 3,347 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 0.20 (3347 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 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: 0.204 AC: 30944 AN: 151972 Hom.: 3339 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.204 AC: 30984 AN: 152090 Hom.: 3347 Cov.: 31 AF XY: 0.202 AC XY: 15001 AN XY: 74372

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.186

Alfa AF: 0.196 Hom.: 379

Bravo AF: 0.217

Asia WGS AF: 0.191 AC: 664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9320815; hg19: chr6-121732490;