rs2183004

Variant names:

• chr9-80640399-G-A
• rs2183004

Your query was ambiguous. Multiple possible variants found:

• chr9-80640399-G-A
• chr9-80640399-G-C

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 0.295 in 151,408 control chromosomes in the GnomAD database, including 7,021 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 0.29 (7021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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: 0.295 AC: 44583 AN: 151292 Hom.: 7011 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.295 AC: 44613 AN: 151408 Hom.: 7021 Cov.: 31 AF XY: 0.303 AC XY: 22436 AN XY: 73936

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.295

Alfa AF: 0.300 Hom.: 4337

Bravo AF: 0.288

Asia WGS AF: 0.484 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2183004; hg19: chr9-83255314;