rs56325233

chr3-128533470-C-Achr3-128533470-C-Gchr3-128533470-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 0.042 (8 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1801 AN: 43294 Hom.: 8 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0727

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0705

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0556

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0317

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 AF: 0.0416 AC: 1801 AN: 43326 Hom.: 8 Cov.: 0 AF XY: 0.0389 AC XY: 809 AN XY: 20800

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0208

Gnomad4 ASJ AF: 0.0705

Gnomad4 EAS AF: 0.0138

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.0315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56325233; hg19: chr3-128252313;