rs580859

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;