rs10511571

chr9-12306011-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 0.0695 in 152,072 control chromosomes in the GnomAD database, including 1,132 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 0.069 (1132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

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 (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.0694 AC: 10541 AN: 151952 Hom.: 1130 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00571

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0695 AC: 10568 AN: 152072 Hom.: 1132 Cov.: 33 AF XY: 0.0669 AC XY: 4970 AN XY: 74344

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0304

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00571

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0443 Hom.: 79

Bravo AF: 0.0781

Asia WGS AF: 0.0510 AC: 177 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511571; hg19: chr9-12306011;