chr10-26214185-A-G

Position:

• chr10-26214185-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;