rs2839520

Positions:

• chr21-42449553-G-A

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 0.466 in 151,786 control chromosomes in the GnomAD database, including 17,200 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 (17200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70700 AN: 151668 Hom.: 17200 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70718 AN: 151786 Hom.: 17200 Cov.: 31 AF XY: 0.468 AC XY: 34734 AN XY: 74160

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.487

Alfa AF: 0.512 Hom.: 41281

Bravo AF: 0.446

Asia WGS AF: 0.490 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839520; hg19: chr21-43869663;