rs2825699

Variant names:

• chr21-19639917-A-C
• rs2825699

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 0.204 in 151,654 control chromosomes in the GnomAD database, including 3,301 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 0.20 (3301 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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: 0.204 AC: 30990 AN: 151540 Hom.: 3300 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.204 AC: 31012 AN: 151654 Hom.: 3301 Cov.: 32 AF XY: 0.207 AC XY: 15312 AN XY: 74122

African (AFR) AF: 0.236 AC: 9790 AN: 41428

American (AMR) AF: 0.181 AC: 2751 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3464

East Asian (EAS) AF: 0.228 AC: 1173 AN: 5150

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1745 AN: 10388

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.185 AC: 12561 AN: 67880

Other (OTH) AF: 0.210 AC: 441 AN: 2104

Alfa AF: 0.192 Hom.: 3658

Bravo AF: 0.205

Asia WGS AF: 0.253 AC: 875 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.45
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs2825699; hg19: chr21-21012231;