rs2828503

Variant names:

• chr21-23754094-G-A
• rs2828503

Your query was ambiguous. Multiple possible variants found:

• chr21-23754094-G-A
• chr21-23754094-G-T

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 0.482 in 151,884 control chromosomes in the GnomAD database, including 17,989 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 0.48 (17989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.482 AC: 73171 AN: 151766 Hom.: 17966 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.482 AC: 73225 AN: 151884 Hom.: 17989 Cov.: 32 AF XY: 0.485 AC XY: 35991 AN XY: 74220

African (AFR) AF: 0.389 AC: 16125 AN: 41402

American (AMR) AF: 0.541 AC: 8246 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1871 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2358 AN: 5156

South Asian (SAS) AF: 0.512 AC: 2473 AN: 4826

European-Finnish (FIN) AF: 0.554 AC: 5823 AN: 10520

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34638 AN: 67954

Other (OTH) AF: 0.483 AC: 1020 AN: 2110

Alfa AF: 0.493 Hom.: 2377

Bravo AF: 0.478

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2828503; hg19: chr21-25126411;