rs10125157

Variant names:

• chr9-118580943-A-C
• rs10125157

Your query was ambiguous. Multiple possible variants found:

• chr9-118580943-A-C
• chr9-118580943-A-G
• chr9-118580943-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;