rs220262

Variant names:

• chr21-42061937-T-A
• rs220262

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 0.443 in 152,062 control chromosomes in the GnomAD database, including 15,404 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 0.44 (15404 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 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: 0.443 AC: 67374 AN: 151944 Hom.: 15391 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.443 AC: 67414 AN: 152062 Hom.: 15404 Cov.: 33 AF XY: 0.438 AC XY: 32537 AN XY: 74344

African (AFR) AF: 0.393 AC: 16302 AN: 41460

American (AMR) AF: 0.580 AC: 8867 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1414 AN: 5168

South Asian (SAS) AF: 0.328 AC: 1583 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4072 AN: 10584

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31884 AN: 67960

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.451 Hom.: 1913

Bravo AF: 0.462

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.82
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs220262; hg19: chr21-43482046;