rs2828155

Variant names:

• chr21-23439462-C-A
• rs2828155

Your query was ambiguous. Multiple possible variants found:

• chr21-23439462-C-A
• chr21-23439462-C-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 0.472 in 149,580 control chromosomes in the GnomAD database, including 17,676 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 0.47 (17676 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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: 0.472 AC: 70525 AN: 149492 Hom.: 17679 Cov.: 30

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.472 AC: 70532 AN: 149580 Hom.: 17676 Cov.: 30 AF XY: 0.473 AC XY: 34499 AN XY: 72896

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.477

Alfa AF: 0.504 Hom.: 9111

Bravo AF: 0.448

Asia WGS AF: 0.463 AC: 1601 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2828155; hg19: chr21-24811782;