rs1459085

Variant names:

• chr5-116994179-G-A
• rs1459085

Your query was ambiguous. Multiple possible variants found:

• chr5-116994179-G-A
• chr5-116994179-G-C
• chr5-116994179-G-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 0.514 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;