chr9-114734370-G-A

Variant names:

• chr9-114734370-G-A
• rs10759734

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 0.777 in 152,006 control chromosomes in the GnomAD database, including 46,075 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 0.78 (46075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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: 0.777 AC: 118087 AN: 151888 Hom.: 46035 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118182 AN: 152006 Hom.: 46075 Cov.: 31 AF XY: 0.782 AC XY: 58118 AN XY: 74322

African (AFR) AF: 0.789 AC: 32701 AN: 41422

American (AMR) AF: 0.774 AC: 11834 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4347 AN: 5184

South Asian (SAS) AF: 0.826 AC: 3983 AN: 4820

European-Finnish (FIN) AF: 0.821 AC: 8663 AN: 10552

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.754 AC: 51237 AN: 67960

Other (OTH) AF: 0.779 AC: 1646 AN: 2112

Alfa AF: 0.769 Hom.: 17318

Bravo AF: 0.775

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.53
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10759734; hg19: chr9-117496650; COSMIC: COSV60395529;