rs2826288

Variant names:

• chr21-20474321-A-G
• rs2826288

Your query was ambiguous. Multiple possible variants found:

• chr21-20474321-A-G
• chr21-20474321-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.151 in 152,084 control chromosomes in the GnomAD database, including 2,028 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 0.15 (2028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.151 AC: 22932 AN: 151966 Hom.: 2027 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.151 AC: 22951 AN: 152084 Hom.: 2028 Cov.: 32 AF XY: 0.147 AC XY: 10943 AN XY: 74344

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.156

Alfa AF: 0.107 Hom.: 587

Bravo AF: 0.157

Asia WGS AF: 0.0670 AC: 234 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	2.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826288; hg19: chr21-21846633;