rs613930

Variant names:

• chr22-20197596-C-A
• rs613930

Your query was ambiguous. Multiple possible variants found:

• chr22-20197596-C-A
• chr22-20197596-C-T

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 0.259 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.240

Alfa AF: 0.189 Hom.: 1595

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

Splicing

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

Publications

LitVar

Other links and lift over

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