chr22-38282740-C-A

Variant names:

• chr22-38282740-C-A
• rs9622773

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 0.138 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0918 AC: 3801 AN: 41414

American (AMR) AF: 0.116 AC: 1769 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.105 AC: 542 AN: 5158

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1384 AN: 10508

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11294 AN: 67952

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.142 Hom.: 486

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9622773; hg19: chr22-38678746;