rs28625386

Positions:

• chr4-69264211-C-G
• chr4-69264211-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 (346 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.00 AC: 28034 AN: 121726 Hom.: 349 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.210

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.230 AC: 28041 AN: 121822 Hom.: 346 Cov.: 30 AF XY: 0.229 AC XY: 13557 AN XY: 59110

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.207

Alfa AF: 0.158 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28625386; hg19: chr4-70129929;