rs580859

Variant names:

• chr13-68558308-A-G
• rs580859

Your query was ambiguous. Multiple possible variants found:

• chr13-68558308-A-G
• chr13-68558308-A-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 0.623 in 151,960 control chromosomes in the GnomAD database, including 30,169 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 0.62 (30169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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: 0.624 AC: 94704 AN: 151842 Hom.: 30160 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.623 AC: 94741 AN: 151960 Hom.: 30169 Cov.: 31 AF XY: 0.617 AC XY: 45817 AN XY: 74268

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.627

Alfa AF: 0.661 Hom.: 4184

Bravo AF: 0.618

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs580859; hg19: chr13-69132440;