rs28625386

Variant names:

• chr4-69264211-C-G
• rs28625386

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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: 0.230 AC: 28034 AN: 121726 Hom.: 349 Cov.: 30

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.186 AC: 5954 AN: 31972

American (AMR) AF: 0.247 AC: 2990 AN: 12090

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 519 AN: 2842

East Asian (EAS) AF: 0.208 AC: 805 AN: 3878

South Asian (SAS) AF: 0.215 AC: 808 AN: 3754

European-Finnish (FIN) AF: 0.238 AC: 1937 AN: 8134

Middle Eastern (MID) AF: 0.147 AC: 32 AN: 218

European-Non Finnish (NFE) AF: 0.255 AC: 14442 AN: 56540

Other (OTH) AF: 0.207 AC: 340 AN: 1642

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.158 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.41
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs28625386; hg19: chr4-70129929;