rs7040869

chr9-99072866-G-A

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 0.118 in 152,120 control chromosomes in the GnomAD database, including 1,340 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 0.12 (1340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17984 AN: 152004 Hom.: 1339 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.118 AC: 17988 AN: 152120 Hom.: 1340 Cov.: 32 AF XY: 0.121 AC XY: 8972 AN XY: 74350

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.147

Alfa AF: 0.117 Hom.: 160

Bravo AF: 0.117

Asia WGS AF: 0.242 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7040869; hg19: chr9-101835148;