rs2040273

chr21-25859887-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 0.65 in 151,944 control chromosomes in the GnomAD database, including 32,732 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 0.65 (32732 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

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 (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.649 AC: 98582 AN: 151826 Hom.: 32674 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.650 AC: 98703 AN: 151944 Hom.: 32732 Cov.: 31 AF XY: 0.653 AC XY: 48482 AN XY: 74264

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.632

Alfa AF: 0.599 Hom.: 12601

Bravo AF: 0.661

Asia WGS AF: 0.691 AC: 2404 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	0.70
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040273; hg19: chr21-27232198;