rs10739579

chr9-120932510-C-Achr9-120932510-C-T

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 0.656 in 152,014 control chromosomes in the GnomAD database, including 32,881 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 0.66 (32881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.794 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: 0.656 AC: 99632 AN: 151896 Hom.: 32841 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.656 AC: 99722 AN: 152014 Hom.: 32881 Cov.: 32 AF XY: 0.658 AC XY: 48865 AN XY: 74310

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.686

Alfa AF: 0.595 Hom.: 3023

Bravo AF: 0.662

Asia WGS AF: 0.766 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.60
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10739579; hg19: chr9-123694788;