rs2822669

Variant names:

• chr21-14458257-C-T
• rs2822669

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 0.183 in 151,668 control chromosomes in the GnomAD database, including 3,972 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 0.18 (3972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.182 AC: 27619 AN: 151550 Hom.: 3949 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.183 AC: 27687 AN: 151668 Hom.: 3972 Cov.: 32 AF XY: 0.180 AC XY: 13371 AN XY: 74110

African (AFR) AF: 0.403 AC: 16659 AN: 41374

American (AMR) AF: 0.116 AC: 1760 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3462

East Asian (EAS) AF: 0.0516 AC: 265 AN: 5140

South Asian (SAS) AF: 0.127 AC: 611 AN: 4820

European-Finnish (FIN) AF: 0.0879 AC: 929 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6459 AN: 67796

Other (OTH) AF: 0.164 AC: 346 AN: 2108

Alfa AF: 0.138 Hom.: 1552

Bravo AF: 0.194

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.49
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2822669; hg19: chr21-15830578;