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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 = 0.000000), 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 v4.3

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;