10-25865536-G-T

Variant names:

• chr10-25865536-G-T
• rs10508706

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 0.322 in 152,026 control chromosomes in the GnomAD database, including 8,104 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 (8104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.322 AC: 48917 AN: 151908 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.322 AC: 48962 AN: 152026 Hom.: 8104 Cov.: 32 AF XY: 0.316 AC XY: 23456 AN XY: 74298

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.324

Alfa AF: 0.231 Hom.: 577

Bravo AF: 0.322

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508706; hg19: chr10-26154465;