rs1799584

Variant names:

• chr5-166391163-A-C
• rs1799584

Your query was ambiguous. Multiple possible variants found:

• chr5-166391163-A-C
• chr5-166391163-A-G
• chr5-166391163-A-T

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 0.325 in 151,878 control chromosomes in the GnomAD database, including 8,187 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 0.33 (8187 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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: 0.325 AC: 49320 AN: 151760 Hom.: 8174 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.325 AC: 49365 AN: 151878 Hom.: 8187 Cov.: 31 AF XY: 0.329 AC XY: 24386 AN XY: 74198

African (AFR) AF: 0.300 AC: 12447 AN: 41424

American (AMR) AF: 0.324 AC: 4940 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2643 AN: 5148

South Asian (SAS) AF: 0.295 AC: 1415 AN: 4792

European-Finnish (FIN) AF: 0.392 AC: 4129 AN: 10522

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22016 AN: 67948

Other (OTH) AF: 0.307 AC: 648 AN: 2112

Alfa AF: 0.321 Hom.: 3071

Bravo AF: 0.323

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1799584; hg19: chr5-165818168;