rs1822590

Variant names:

• chr8-52988236-C-A
• rs1822590

Your query was ambiguous. Multiple possible variants found:

• chr8-52988236-C-A
• chr8-52988236-C-G
• chr8-52988236-C-T

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 0.325 in 151,210 control chromosomes in the GnomAD database, including 8,385 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 0.33 (8385 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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: 0.325 AC: 49105 AN: 151100 Hom.: 8362 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.325 AC: 49174 AN: 151210 Hom.: 8385 Cov.: 31 AF XY: 0.323 AC XY: 23873 AN XY: 73892

African (AFR) AF: 0.432 AC: 17823 AN: 41282

American (AMR) AF: 0.253 AC: 3812 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 853 AN: 3460

East Asian (EAS) AF: 0.302 AC: 1552 AN: 5134

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4806

European-Finnish (FIN) AF: 0.299 AC: 3136 AN: 10502

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19793 AN: 67676

Other (OTH) AF: 0.325 AC: 682 AN: 2098

Alfa AF: 0.305 Hom.: 12133

Bravo AF: 0.329

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.089
DANN	Benign	0.56
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1822590; hg19: chr8-53900796; COSMIC: COSV65668611;