rs9320815

Variant names:

• chr6-121411344-A-G
• rs9320815

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 0.204 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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

African (AFR) AF: 0.229 AC: 9488 AN: 41476

American (AMR) AF: 0.273 AC: 4167 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3466

East Asian (EAS) AF: 0.182 AC: 942 AN: 5172

South Asian (SAS) AF: 0.134 AC: 646 AN: 4828

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10590

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13059 AN: 67988

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.197 Hom.: 403

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs9320815; hg19: chr6-121732490;