rs9969729

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;