rs10739579

Variant names:

• chr9-120932510-C-A
• rs10739579

Your query was ambiguous. Multiple possible variants found:

• chr9-120932510-C-A
• chr9-120932510-C-T

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 0.656 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.650 AC: 26951 AN: 41450

American (AMR) AF: 0.692 AC: 10559 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3725 AN: 5172

South Asian (SAS) AF: 0.815 AC: 3932 AN: 4824

European-Finnish (FIN) AF: 0.576 AC: 6087 AN: 10564

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43757 AN: 67948

Other (OTH) AF: 0.686 AC: 1451 AN: 2114

Alfa AF: 0.615 Hom.: 4252

Bravo AF: 0.662

Asia WGS AF: 0.766 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.60
DANN	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10739579; hg19: chr9-123694788; COSMIC: COSV107491371;