rs10512384

Variant names:

• chr9-108693095-T-C
• rs10512384

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0768 AC: 3192 AN: 41556

American (AMR) AF: 0.0990 AC: 1513 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.0428 AC: 222 AN: 5186

South Asian (SAS) AF: 0.195 AC: 942 AN: 4824

European-Finnish (FIN) AF: 0.0949 AC: 1007 AN: 10616

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10829 AN: 68006

Other (OTH) AF: 0.132 AC: 278 AN: 2114

Alfa AF: 0.137 Hom.: 719

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10512384; hg19: chr9-111455375;