rs1822881

Variant names:

• chr2-145286484-A-G
• rs1822881

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 0.282 in 151,756 control chromosomes in the GnomAD database, including 6,225 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 0.28 (6225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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: 0.282 AC: 42827 AN: 151638 Hom.: 6226 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.282 AC: 42831 AN: 151756 Hom.: 6225 Cov.: 32 AF XY: 0.280 AC XY: 20790 AN XY: 74156

African (AFR) AF: 0.253 AC: 10463 AN: 41426

American (AMR) AF: 0.291 AC: 4438 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3464

East Asian (EAS) AF: 0.118 AC: 600 AN: 5098

South Asian (SAS) AF: 0.305 AC: 1466 AN: 4808

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10586

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20880 AN: 67820

Other (OTH) AF: 0.284 AC: 599 AN: 2110

Alfa AF: 0.301 Hom.: 31541

Bravo AF: 0.279

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs1822881; hg19: chr2-146044052;