rs2839350

Variant names:

• chr21-46597307-G-A
• rs2839350

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 0.214 in 152,140 control chromosomes in the GnomAD database, including 3,788 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 0.21 (3788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.214 AC: 32495 AN: 152022 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.214 AC: 32537 AN: 152140 Hom.: 3788 Cov.: 32 AF XY: 0.213 AC XY: 15823 AN XY: 74386

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.212

Alfa AF: 0.194 Hom.: 3098

Bravo AF: 0.207

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839350; hg19: chr21-48017220;