rs220263

Variant names:

• chr21-42062052-G-A
• rs220263

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 0.509 in 151,984 control chromosomes in the GnomAD database, including 20,374 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 0.51 (20374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.655 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: 0.509 AC: 77369 AN: 151866 Hom.: 20366 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.509 AC: 77405 AN: 151984 Hom.: 20374 Cov.: 32 AF XY: 0.505 AC XY: 37480 AN XY: 74274

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.521

Alfa AF: 0.525 Hom.: 2052

Bravo AF: 0.529

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs220263; hg19: chr21-43482161;