rs1799584

chr5-166391163-A-Cchr5-166391163-A-Gchr5-166391163-A-T

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 0.325 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.307

Alfa AF: 0.323 Hom.: 2017

Bravo AF: 0.323

Asia WGS AF: 0.380 AC: 1320 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	10
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799584; hg19: chr5-165818168;