rs2422245

Variant names:

• chr2-64515132-C-A
• rs2422245

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 0.47 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

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 (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.469 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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.453

Alfa AF: 0.379 Hom.: 6568

Bravo AF: 0.491

Asia WGS AF: 0.535 AC: 1860 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	0.56
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2422245; hg19: chr2-64742266;