rs159729

chr5-58886317-G-Achr5-58886317-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;