rs4280803

Variant names:

• chr4-56894258-G-T
• rs4280803

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 0.0836 in 152,146 control chromosomes in the GnomAD database, including 819 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 0.084 (819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 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: 0.0836 AC: 12702 AN: 152028 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0836 AC: 12713 AN: 152146 Hom.: 819 Cov.: 32 AF XY: 0.0858 AC XY: 6383 AN XY: 74382

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.0708

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0676 Hom.: 65

Bravo AF: 0.0985

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4280803; hg19: chr4-57760424;