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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.188 AC: 7800 AN: 41528

American (AMR) AF: 0.261 AC: 3990 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3055 AN: 5178

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2006 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19929 AN: 67968

Other (OTH) AF: 0.270 AC: 570 AN: 2114

Alfa AF: 0.278 Hom.: 4845

Bravo AF: 0.270

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs284793; hg19: chr4-100330294;