rs2406040

Variant names:

• chr4-136669735-T-C
• rs2406040

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 0.26 in 152,084 control chromosomes in the GnomAD database, including 5,210 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 0.26 (5210 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.260 AC: 39551 AN: 151966 Hom.: 5204 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.260 AC: 39594 AN: 152084 Hom.: 5210 Cov.: 33 AF XY: 0.259 AC XY: 19260 AN XY: 74344

African (AFR) AF: 0.273 AC: 11335 AN: 41476

American (AMR) AF: 0.230 AC: 3506 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1516 AN: 5164

South Asian (SAS) AF: 0.212 AC: 1024 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10584

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18083 AN: 67976

Other (OTH) AF: 0.245 AC: 516 AN: 2110

Alfa AF: 0.256 Hom.: 13223

Bravo AF: 0.258

Asia WGS AF: 0.251 AC: 873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2406040; hg19: chr4-137590890;