21-42062052-G-A

Variant names:

• chr21-42062052-G-A
• rs220263

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 0.509 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.406 AC: 16850 AN: 41458

American (AMR) AF: 0.666 AC: 10162 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2684 AN: 5166

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4547 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37335 AN: 67946

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.545 Hom.: 97822

Bravo AF: 0.529

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.57
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs220263; hg19: chr21-43482161;