rs283406

Variant names:

• chr4-99377314-G-A
• rs283406

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 0.0743 in 152,104 control chromosomes in the GnomAD database, including 470 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 0.074 (470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.08 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: 0.0743 AC: 11291 AN: 151986 Hom.: 469 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0200

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0743 AC: 11303 AN: 152104 Hom.: 470 Cov.: 32 AF XY: 0.0729 AC XY: 5422 AN XY: 74336

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.0677

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0198

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0732 Hom.: 88

Bravo AF: 0.0743

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283406; hg19: chr4-100298471; COSMIC: COSV65399659;