rs184946

Variant names:

• chr5-158652386-C-T
• rs184946

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.313 in 151,980 control chromosomes in the GnomAD database, including 7,798 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 0.31 (7798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.98
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 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: 0.313 AC: 47590 AN: 151862 Hom.: 7796 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.313 AC: 47606 AN: 151980 Hom.: 7798 Cov.: 32 AF XY: 0.309 AC XY: 22962 AN XY: 74260

African (AFR) AF: 0.289 AC: 11970 AN: 41448

American (AMR) AF: 0.279 AC: 4260 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3470

East Asian (EAS) AF: 0.0458 AC: 237 AN: 5170

South Asian (SAS) AF: 0.200 AC: 961 AN: 4810

European-Finnish (FIN) AF: 0.369 AC: 3890 AN: 10548

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24349 AN: 67964

Other (OTH) AF: 0.309 AC: 651 AN: 2106

Alfa AF: 0.343 Hom.: 29549

Bravo AF: 0.307

Asia WGS AF: 0.137 AC: 480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	23
DANN	Benign	0.59
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs184946; hg19: chr5-158079394;