rs7286586

Variant names:

• chr22-49408460-A-C
• rs7286586

Your query was ambiguous. Multiple possible variants found:

• chr22-49408460-A-C
• chr22-49408460-A-G

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 0.269 in 152,036 control chromosomes in the GnomAD database, including 7,293 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 0.27 (7293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.269 AC: 40839 AN: 151918 Hom.: 7278 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.269 AC: 40889 AN: 152036 Hom.: 7293 Cov.: 32 AF XY: 0.273 AC XY: 20253 AN XY: 74318

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.252

Alfa AF: 0.166 Hom.: 2618

Bravo AF: 0.284

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7286586; hg19: chr22-49802109;