rs10906115

Variant names:

• chr10-12272998-A-G
• rs10906115

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 0.374 in 151,934 control chromosomes in the GnomAD database, including 10,992 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 0.37 (10992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 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: 0.374 AC: 56772 AN: 151816 Hom.: 10980 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.374 AC: 56822 AN: 151934 Hom.: 10992 Cov.: 31 AF XY: 0.378 AC XY: 28027 AN XY: 74240

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.378

Alfa AF: 0.391 Hom.: 27492

Bravo AF: 0.370

Asia WGS AF: 0.471 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10906115; hg19: chr10-12314997;