rs9609565

Variant names:

• chr22-32471541-G-A
• rs9609565

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 0.239 in 151,992 control chromosomes in the GnomAD database, including 4,816 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 0.24 (4816 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.240 AC: 36374 AN: 151874 Hom.: 4812 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.239 AC: 36392 AN: 151992 Hom.: 4816 Cov.: 31 AF XY: 0.242 AC XY: 17964 AN XY: 74274

African (AFR) AF: 0.124 AC: 5137 AN: 41444

American (AMR) AF: 0.262 AC: 4009 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 963 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5168

South Asian (SAS) AF: 0.170 AC: 817 AN: 4818

European-Finnish (FIN) AF: 0.343 AC: 3621 AN: 10548

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19967 AN: 67944

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.441 Hom.: 7983

Bravo AF: 0.229

Asia WGS AF: 0.228 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs9609565; hg19: chr22-32867528;