9-113382693-G-A

Variant names:

• chr9-113382693-G-A
• rs818702

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 0.783 in 152,204 control chromosomes in the GnomAD database, including 46,978 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 (46978 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.782 AC: 118994 AN: 152086 Hom.: 46932 Cov.: 34

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.783 AC: 119100 AN: 152204 Hom.: 46978 Cov.: 34 AF XY: 0.778 AC XY: 57863 AN XY: 74410

African (AFR) AF: 0.838 AC: 34784 AN: 41528

American (AMR) AF: 0.692 AC: 10574 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2967 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2664 AN: 5174

South Asian (SAS) AF: 0.676 AC: 3262 AN: 4826

European-Finnish (FIN) AF: 0.805 AC: 8537 AN: 10606

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53688 AN: 68000

Other (OTH) AF: 0.781 AC: 1650 AN: 2112

Alfa AF: 0.787 Hom.: 90079

Bravo AF: 0.776

Asia WGS AF: 0.639 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.14
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs818702; hg19: chr9-116144973;