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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.599 AC: 24866 AN: 41488

American (AMR) AF: 0.348 AC: 5320 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3202 AN: 5172

South Asian (SAS) AF: 0.372 AC: 1796 AN: 4822

European-Finnish (FIN) AF: 0.407 AC: 4301 AN: 10560

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20078 AN: 67986

Other (OTH) AF: 0.343 AC: 724 AN: 2112

Alfa AF: 0.309 Hom.: 6606

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs159729; hg19: chr5-58182144;