rs4680878

Variant names:

• chr3-30152052-T-G
• rs4680878

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 0.35 in 151,982 control chromosomes in the GnomAD database, including 9,417 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 0.35 (9417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

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: 0.350 AC: 53143 AN: 151864 Hom.: 9406 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.350 AC: 53175 AN: 151982 Hom.: 9417 Cov.: 32 AF XY: 0.352 AC XY: 26117 AN XY: 74288

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.337

Alfa AF: 0.349 Hom.: 4163

Bravo AF: 0.345

Asia WGS AF: 0.373 AC: 1294 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4680878; hg19: chr3-30193543;