rs10125685

Positions:

• chr9-104019938-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;