chr4-135769745-T-G

Position:

• chr4-135769745-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.212

Alfa AF: 0.149 Hom.: 878

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2174387; hg19: chr4-136690900;