rs2209907

Variant names:

• chr9-80554440-A-G
• rs2209907

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 0.131 in 151,938 control chromosomes in the GnomAD database, including 1,480 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 0.13 (1480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.131 AC: 19947 AN: 151820 Hom.: 1477 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.131 AC: 19974 AN: 151938 Hom.: 1480 Cov.: 33 AF XY: 0.131 AC XY: 9756 AN XY: 74268

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.140

Alfa AF: 0.114 Hom.: 2191

Bravo AF: 0.135

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209907; hg19: chr9-83169355;