rs10125157

chr9-118580943-A-Cchr9-118580943-A-Gchr9-118580943-A-T

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 0.0871 in 152,024 control chromosomes in the GnomAD database, including 806 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 0.087 (806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.0871 AC: 13230 AN: 151906 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.0871 AC: 13236 AN: 152024 Hom.: 806 Cov.: 32 AF XY: 0.0924 AC XY: 6870 AN XY: 74314

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.0448 Hom.: 52

Bravo AF: 0.0879

Asia WGS AF: 0.218 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.6
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10125157; hg19: chr9-121343221;