rs2209907

Variant names:

• chr9-80554440-A-G
• rs2209907

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.190 AC: 7875 AN: 41478

American (AMR) AF: 0.0930 AC: 1418 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1002 AN: 5122

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1256 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7159 AN: 67898

Other (OTH) AF: 0.140 AC: 296 AN: 2108

Alfa AF: 0.117 Hom.: 3633

Bravo AF: 0.135

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2209907; hg19: chr9-83169355;