rs10906115

Positions:

• chr10-12272998-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 0.374 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;