9-105869669-G-A

Variant names:

• chr9-105869669-G-A
• rs9969729

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 0.271 in 151,992 control chromosomes in the GnomAD database, including 8,022 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 0.27 (8022 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41047 AN: 151874 Hom.: 7984 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.271 AC: 41146 AN: 151992 Hom.: 8022 Cov.: 32 AF XY: 0.271 AC XY: 20133 AN XY: 74318

African (AFR) AF: 0.523 AC: 21661 AN: 41392

American (AMR) AF: 0.277 AC: 4228 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2822 AN: 5172

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8539 AN: 67992

Other (OTH) AF: 0.255 AC: 537 AN: 2106

Alfa AF: 0.200 Hom.: 7983

Bravo AF: 0.297

Asia WGS AF: 0.415 AC: 1439 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	1.6
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9969729; hg19: chr9-108631950;