rs1022442

Positions:

• chr21-20983528-G-A

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 0.393 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.393

Alfa AF: 0.387 Hom.: 21891

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022442; hg19: chr21-22355846;