rs2183004

chr9-80640399-G-Achr9-80640399-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;