3-183589056-G-T

Variant names:

• chr3-183589056-G-T
• rs9290762

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 0.187 in 152,100 control chromosomes in the GnomAD database, including 3,997 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 0.19 (3997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28476 AN: 151982 Hom.: 3992 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.187 AC: 28510 AN: 152100 Hom.: 3997 Cov.: 31 AF XY: 0.183 AC XY: 13583 AN XY: 74366

African (AFR) AF: 0.387 AC: 16027 AN: 41454

American (AMR) AF: 0.169 AC: 2579 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1297 AN: 5162

South Asian (SAS) AF: 0.103 AC: 499 AN: 4822

European-Finnish (FIN) AF: 0.0551 AC: 584 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0928 AC: 6310 AN: 67998

Other (OTH) AF: 0.179 AC: 377 AN: 2102

Alfa AF: 0.0726 Hom.: 146

Bravo AF: 0.207

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.52
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs9290762; hg19: chr3-183306844;