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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.474 AC: 19651 AN: 41426

American (AMR) AF: 0.232 AC: 3545 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2765 AN: 5150

South Asian (SAS) AF: 0.420 AC: 2021 AN: 4810

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9998 AN: 67966

Other (OTH) AF: 0.252 AC: 534 AN: 2116

Alfa AF: 0.190 Hom.: 5331

Bravo AF: 0.284

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7286586; hg19: chr22-49802109;