rs10512384

chr9-108693095-T-C

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 0.124 in 152,264 control chromosomes in the GnomAD database, including 1,350 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 (1350 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.124 AC: 18874 AN: 152146 Hom.: 1350 Cov.: 33

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.124 AC: 18874 AN: 152264 Hom.: 1350 Cov.: 33 AF XY: 0.121 AC XY: 9016 AN XY: 74448

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.132

Alfa AF: 0.138 Hom.: 610

Bravo AF: 0.121

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	3.1
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512384; hg19: chr9-111455375;