rs9606232

chr22-20077847-G-A

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 0.18 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.216

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

Publications

LitVar

Other links and lift over

dbSNP: rs9606232; hg19: chr22-20065370;