rs2406342

Variant names:

• chr18-76776324-G-T
• rs2406342

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 0.426 in 152,112 control chromosomes in the GnomAD database, including 13,868 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 0.43 (13868 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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: 0.426 AC: 64759 AN: 151994 Hom.: 13848 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.426 AC: 64819 AN: 152112 Hom.: 13868 Cov.: 33 AF XY: 0.428 AC XY: 31796 AN XY: 74348

African (AFR) AF: 0.439 AC: 18225 AN: 41504

American (AMR) AF: 0.407 AC: 6214 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2547 AN: 5174

South Asian (SAS) AF: 0.461 AC: 2218 AN: 4812

European-Finnish (FIN) AF: 0.453 AC: 4790 AN: 10568

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28173 AN: 67978

Other (OTH) AF: 0.411 AC: 869 AN: 2116

Alfa AF: 0.413 Hom.: 44500

Bravo AF: 0.420

Asia WGS AF: 0.426 AC: 1482 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	0.15
DANN	Benign	0.69
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2406342; hg19: chr18-74488280;