rs3808900

Positions:

• chr9-122230485-A-G

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 0.229 in 152,228 control chromosomes in the GnomAD database, including 4,132 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 0.23 (4132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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: 0.229 AC: 34800 AN: 152108 Hom.: 4135 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.229 AC: 34794 AN: 152228 Hom.: 4132 Cov.: 33 AF XY: 0.230 AC XY: 17121 AN XY: 74426

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.230

Alfa AF: 0.245 Hom.: 6542

Bravo AF: 0.231

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808900; hg19: chr9-124992764;