rs1022442

Variant names:

• chr21-20983528-G-A
• rs1022442

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 0.393 in 151,932 control chromosomes in the GnomAD database, including 11,996 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 0.39 (11996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.393 AC: 59660 AN: 151814 Hom.: 11984 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.393 AC: 59717 AN: 151932 Hom.: 11996 Cov.: 32 AF XY: 0.396 AC XY: 29377 AN XY: 74244

African (AFR) AF: 0.417 AC: 17269 AN: 41460

American (AMR) AF: 0.337 AC: 5147 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1311 AN: 5120

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4812

European-Finnish (FIN) AF: 0.443 AC: 4673 AN: 10542

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26638 AN: 67944

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.387 Hom.: 34459

Bravo AF: 0.384

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0010
DANN	Benign	0.44
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1022442; hg19: chr21-22355846;