rs2839670

chr10-26215411-C-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 0.318 in 152,206 control chromosomes in the GnomAD database, including 11,104 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 0.32 (11104 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 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: 0.318 AC: 48376 AN: 152088 Hom.: 11088 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.318 AC: 48436 AN: 152206 Hom.: 11104 Cov.: 33 AF XY: 0.316 AC XY: 23509 AN XY: 74418

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.307

Alfa AF: 0.210 Hom.: 2024

Bravo AF: 0.345

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839670; hg19: chr10-26504340;