rs9622773

chr22-38282740-C-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 0.138 in 151,860 control chromosomes in the GnomAD database, including 1,618 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 0.14 (1618 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 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: 0.139 AC: 21024 AN: 151742 Hom.: 1619 Cov.: 30

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.138 AC: 21016 AN: 151860 Hom.: 1618 Cov.: 30 AF XY: 0.138 AC XY: 10244 AN XY: 74200

Gnomad4 AFR AF: 0.0918

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.139

Alfa AF: 0.143 Hom.: 484

Bravo AF: 0.130

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.17
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9622773; hg19: chr22-38678746;