chr10-26215411-C-A

Variant names:

• chr10-26215411-C-A
• rs2839670

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.648 AC: 26887 AN: 41516

American (AMR) AF: 0.256 AC: 3915 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1646 AN: 5174

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10604

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11910 AN: 68000

Other (OTH) AF: 0.307 AC: 648 AN: 2114

Alfa AF: 0.213 Hom.: 2355

Bravo AF: 0.345

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.41
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2839670; hg19: chr10-26504340;