4-28730859-C-T

Variant names:

• chr4-28730859-C-T
• rs2309883

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 0.251 in 151,942 control chromosomes in the GnomAD database, including 6,265 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 0.25 (6265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 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: 0.251 AC: 38118 AN: 151824 Hom.: 6252 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.251 AC: 38133 AN: 151942 Hom.: 6265 Cov.: 32 AF XY: 0.260 AC XY: 19278 AN XY: 74244

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.283

Alfa AF: 0.276 Hom.: 8035

Bravo AF: 0.249

Asia WGS AF: 0.523 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309883; hg19: chr4-28732481;