rs159729

Variant names:

• chr5-58886317-G-A
• rs159729

Your query was ambiguous. Multiple possible variants found:

• chr5-58886317-G-A
• chr5-58886317-G-C

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 0.405 in 152,110 control chromosomes in the GnomAD database, including 13,926 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 0.40 (13926 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.405 AC: 61505 AN: 151992 Hom.: 13895 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.405 AC: 61583 AN: 152110 Hom.: 13926 Cov.: 33 AF XY: 0.408 AC XY: 30367 AN XY: 74342

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.343

Alfa AF: 0.297 Hom.: 4745

Bravo AF: 0.409

Asia WGS AF: 0.490 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159729; hg19: chr5-58182144;