10-26214185-A-G

Variant names:

• chr10-26214185-A-G
• rs2839668

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 0.0737 in 152,264 control chromosomes in the GnomAD database, including 423 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 0.074 (423 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0838 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: 0.0738 AC: 11230 AN: 152146 Hom.: 423 Cov.: 33

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0737 AC: 11226 AN: 152264 Hom.: 423 Cov.: 33 AF XY: 0.0722 AC XY: 5375 AN XY: 74464

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.0792

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.0502

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0345 Hom.: 17

Bravo AF: 0.0756

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	13
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839668; hg19: chr10-26503114;