rs7040869

Variant names:

• chr9-99072866-G-A
• rs7040869

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;