rs2825388

Variant names:

• chr21-19164331-T-A
• rs2825388

Your query was ambiguous. Multiple possible variants found:

• chr21-19164331-T-A
• chr21-19164331-T-G

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 0.407 in 151,996 control chromosomes in the GnomAD database, including 12,881 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 0.41 (12881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.407 AC: 61808 AN: 151878 Hom.: 12877 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.407 AC: 61853 AN: 151996 Hom.: 12881 Cov.: 32 AF XY: 0.406 AC XY: 30149 AN XY: 74310

African (AFR) AF: 0.406 AC: 16838 AN: 41452

American (AMR) AF: 0.377 AC: 5747 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3464

East Asian (EAS) AF: 0.671 AC: 3464 AN: 5164

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4822

European-Finnish (FIN) AF: 0.402 AC: 4246 AN: 10562

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27666 AN: 67962

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.415 Hom.: 7396

Bravo AF: 0.413

Asia WGS AF: 0.466 AC: 1620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.046
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2825388; hg19: chr21-20536649;