22-20197596-C-A

Variant names:

• chr22-20197596-C-A
• rs613930

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 0.259 in 152,104 control chromosomes in the GnomAD database, including 5,608 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 0.26 (5608 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.259 AC: 39374 AN: 151986 Hom.: 5597 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.259 AC: 39406 AN: 152104 Hom.: 5608 Cov.: 33 AF XY: 0.262 AC XY: 19470 AN XY: 74342

African (AFR) AF: 0.374 AC: 15502 AN: 41470

American (AMR) AF: 0.210 AC: 3205 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1750 AN: 5170

South Asian (SAS) AF: 0.199 AC: 960 AN: 4830

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13591 AN: 67980

Other (OTH) AF: 0.240 AC: 507 AN: 2112

Alfa AF: 0.192 Hom.: 1813

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.60
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs613930; hg19: chr22-20185119; COSMIC: COSV72477993;