rs2426936

Variant names:

• chr20-60900825-T-A
• rs2426936

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 0.244 in 152,020 control chromosomes in the GnomAD database, including 4,857 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 0.24 (4857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.245 AC: 37147 AN: 151902 Hom.: 4853 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.244 AC: 37165 AN: 152020 Hom.: 4857 Cov.: 32 AF XY: 0.236 AC XY: 17579 AN XY: 74330

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.243

Alfa AF: 0.264 Hom.: 765

Bravo AF: 0.243

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.22
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2426936; hg19: chr20-59475881;