rs2423297

Variant names:

• chr20-7840844-G-A
• rs2423297

Your query was ambiguous. Multiple possible variants found:

• chr20-7840844-G-A
• chr20-7840844-G-C

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 0.336 in 151,920 control chromosomes in the GnomAD database, including 9,673 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 0.34 (9673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50993 AN: 151802 Hom.: 9645 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.336 AC: 51077 AN: 151920 Hom.: 9673 Cov.: 32 AF XY: 0.334 AC XY: 24798 AN XY: 74272

African (AFR) AF: 0.501 AC: 20729 AN: 41398

American (AMR) AF: 0.326 AC: 4964 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1675 AN: 5152

South Asian (SAS) AF: 0.488 AC: 2353 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2172 AN: 10574

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16925 AN: 67940

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.273 Hom.: 2671

Bravo AF: 0.352

Asia WGS AF: 0.454 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.41
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2423297; hg19: chr20-7821491;