rs10125685

Variant names:

• chr9-104019938-C-A
• rs10125685

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 0.121 in 151,764 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.121 AC: 18349 AN: 151646 Hom.: 1266 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.121 AC: 18382 AN: 151764 Hom.: 1268 Cov.: 32 AF XY: 0.123 AC XY: 9105 AN XY: 74138

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.0879

Gnomad4 OTH AF: 0.112

Alfa AF: 0.103 Hom.: 182

Bravo AF: 0.119

Asia WGS AF: 0.126 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10125685; hg19: chr9-106782219;