rs284793

Variant names:

• chr4-99409137-G-A
• rs284793

Your query was ambiguous. Multiple possible variants found:

• chr4-99409137-G-A
• chr4-99409137-G-C

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 0.268 in 152,128 control chromosomes in the GnomAD database, including 5,954 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 0.27 (5954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.268 AC: 40779 AN: 152010 Hom.: 5955 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.268 AC: 40796 AN: 152128 Hom.: 5954 Cov.: 32 AF XY: 0.269 AC XY: 19974 AN XY: 74368

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.270

Alfa AF: 0.279 Hom.: 4030

Bravo AF: 0.270

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284793; hg19: chr4-100330294;