rs3808900

Variant names:

• chr9-122230485-A-G
• rs3808900

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 0.229 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.168 AC: 6982 AN: 41538

American (AMR) AF: 0.277 AC: 4234 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1635 AN: 5174

South Asian (SAS) AF: 0.200 AC: 968 AN: 4830

European-Finnish (FIN) AF: 0.236 AC: 2502 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16954 AN: 68020

Other (OTH) AF: 0.230 AC: 485 AN: 2110

Alfa AF: 0.243 Hom.: 8118

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
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs3808900; hg19: chr9-124992764;