rs2838271

Positions:

• chr21-43341994-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 0.225 in 151,954 control chromosomes in the GnomAD database, including 3,951 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 0.23 (3951 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

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 = 0.256 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: 0.225 AC: 34183 AN: 151834 Hom.: 3947 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.225 AC: 34220 AN: 151954 Hom.: 3951 Cov.: 33 AF XY: 0.220 AC XY: 16328 AN XY: 74272

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.222

Alfa AF: 0.228 Hom.: 5513

Bravo AF: 0.227

Asia WGS AF: 0.183 AC: 639 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	2.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838271; hg19: chr21-44761874;