chr20-60900825-T-A

Variant names:

• chr20-60900825-T-A
• rs2426936

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 0.244 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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

African (AFR) AF: 0.213 AC: 8849 AN: 41450

American (AMR) AF: 0.226 AC: 3458 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5176

South Asian (SAS) AF: 0.163 AC: 785 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2256 AN: 10566

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19872 AN: 67966

Other (OTH) AF: 0.243 AC: 513 AN: 2108

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
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs2426936; hg19: chr20-59475881;