rs10960752

chr9-12675284-G-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 0.433 in 151,818 control chromosomes in the GnomAD database, including 18,164 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 0.43 (18164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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: 0.433 AC: 65720 AN: 151700 Hom.: 18164 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.433 AC: 65736 AN: 151818 Hom.: 18164 Cov.: 32 AF XY: 0.427 AC XY: 31662 AN XY: 74176

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.433

Alfa AF: 0.547 Hom.: 4395

Bravo AF: 0.396

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0080
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10960752; hg19: chr9-12675284;