rs2422245

Variant names:

• chr2-64515132-C-A
• rs2422245

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 0.47 in 151,736 control chromosomes in the GnomAD database, including 20,147 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 0.47 (20147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• 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 (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.469 AC: 71169 AN: 151620 Hom.: 20087 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.470 AC: 71293 AN: 151736 Hom.: 20147 Cov.: 32 AF XY: 0.469 AC XY: 34739 AN XY: 74088

African (AFR) AF: 0.802 AC: 33210 AN: 41402

American (AMR) AF: 0.387 AC: 5897 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2625 AN: 5164

South Asian (SAS) AF: 0.514 AC: 2477 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2763 AN: 10396

Middle Eastern (MID) AF: 0.379 AC: 110 AN: 290

European-Non Finnish (NFE) AF: 0.317 AC: 21550 AN: 67928

Other (OTH) AF: 0.453 AC: 954 AN: 2106

Alfa AF: 0.380 Hom.: 7325

Bravo AF: 0.491

Asia WGS AF: 0.535 AC: 1860 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	0.56
DANN	Benign	0.23
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs2422245; hg19: chr2-64742266;