rs2309966

Variant names:

• chr9-71500428-A-C
• rs2309966

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 0.613 in 151,462 control chromosomes in the GnomAD database, including 28,966 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 0.61 (28966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.613 AC: 92819 AN: 151344 Hom.: 28927 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.613 AC: 92916 AN: 151462 Hom.: 28966 Cov.: 32 AF XY: 0.608 AC XY: 44984 AN XY: 73968

African (AFR) AF: 0.744 AC: 30705 AN: 41258

American (AMR) AF: 0.659 AC: 10029 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2030 AN: 3462

East Asian (EAS) AF: 0.534 AC: 2751 AN: 5148

South Asian (SAS) AF: 0.548 AC: 2644 AN: 4822

European-Finnish (FIN) AF: 0.487 AC: 5103 AN: 10480

Middle Eastern (MID) AF: 0.514 AC: 149 AN: 290

European-Non Finnish (NFE) AF: 0.558 AC: 37827 AN: 67782

Other (OTH) AF: 0.625 AC: 1307 AN: 2092

Alfa AF: 0.584 Hom.: 58743

Bravo AF: 0.635

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.32
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2309966; hg19: chr9-74115344;