rs9969729

Variant names:

• chr9-105869669-G-A
• rs9969729

Your query was ambiguous. Multiple possible variants found:

• chr9-105869669-G-A
• chr9-105869669-G-C

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 0.271 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.255

Alfa AF: 0.177 Hom.: 787

Bravo AF: 0.297

Asia WGS AF: 0.415 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9969729; hg19: chr9-108631950;