rs2340392

Variant names:

• chr3-80309150-G-A
• rs2340392

Your query was ambiguous. Multiple possible variants found:

• chr3-80309150-G-A
• chr3-80309150-G-T

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 0.238 in 152,100 control chromosomes in the GnomAD database, including 4,667 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 0.24 (4667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 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: 0.238 AC: 36162 AN: 151982 Hom.: 4658 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.238 AC: 36204 AN: 152100 Hom.: 4667 Cov.: 32 AF XY: 0.244 AC XY: 18122 AN XY: 74358

African (AFR) AF: 0.187 AC: 7778 AN: 41514

American (AMR) AF: 0.338 AC: 5155 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3466

East Asian (EAS) AF: 0.0780 AC: 403 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4810

European-Finnish (FIN) AF: 0.258 AC: 2728 AN: 10572

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.243 AC: 16514 AN: 67992

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.139 Hom.: 244

Bravo AF: 0.239

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2340392; hg19: chr3-80358300;