4-135769745-T-G

Variant names:

• chr4-135769745-T-G
• rs2174387

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 0.226 in 151,962 control chromosomes in the GnomAD database, including 4,394 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 0.23 (4394 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34293 AN: 151842 Hom.: 4383 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.226 AC: 34360 AN: 151962 Hom.: 4394 Cov.: 33 AF XY: 0.233 AC XY: 17292 AN XY: 74272

African (AFR) AF: 0.319 AC: 13241 AN: 41448

American (AMR) AF: 0.297 AC: 4530 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1709 AN: 5146

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2319 AN: 10570

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10262 AN: 67962

Other (OTH) AF: 0.212 AC: 446 AN: 2104

Alfa AF: 0.151 Hom.: 1021

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2174387; hg19: chr4-136690900;