rs9606232

Variant names:

• chr22-20077847-G-A
• rs9606232

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 0.18 in 152,068 control chromosomes in the GnomAD database, including 3,107 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 0.18 (3107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.268 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: 0.180 AC: 27378 AN: 151950 Hom.: 3107 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.180 AC: 27380 AN: 152068 Hom.: 3107 Cov.: 32 AF XY: 0.179 AC XY: 13284 AN XY: 74310

African (AFR) AF: 0.0490 AC: 2031 AN: 41408

American (AMR) AF: 0.175 AC: 2665 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1105 AN: 3472

East Asian (EAS) AF: 0.0651 AC: 338 AN: 5190

South Asian (SAS) AF: 0.280 AC: 1354 AN: 4830

European-Finnish (FIN) AF: 0.202 AC: 2140 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17013 AN: 67998

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.200 Hom.: 501

Bravo AF: 0.171

Asia WGS AF: 0.174 AC: 604 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	0.64
DANN	Benign	0.40

Splicing

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

Other links and lift over

dbSNP: rs9606232; hg19: chr22-20065370;