rs220262

Variant names:

• chr21-42061937-T-A
• rs220262

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 0.443 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.443 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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.446

Alfa AF: 0.461 Hom.: 1506

Bravo AF: 0.462

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
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: rs220262; hg19: chr21-43482046;