rs1459085

chr5-116994179-G-A

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 0.514 in 151,978 control chromosomes in the GnomAD database, including 21,062 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 0.51 (21062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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: 0.514 AC: 78062 AN: 151860 Hom.: 21051 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.514 AC: 78124 AN: 151978 Hom.: 21062 Cov.: 32 AF XY: 0.507 AC XY: 37677 AN XY: 74270

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.506

Alfa AF: 0.470 Hom.: 28399

Bravo AF: 0.529

Asia WGS AF: 0.387 AC: 1344 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459085; hg19: chr5-116329875;