13-68558308-A-G

Variant names:

• chr13-68558308-A-G
• rs580859

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 0.623 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.496 AC: 20553 AN: 41434

American (AMR) AF: 0.649 AC: 9889 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2173 AN: 3472

East Asian (EAS) AF: 0.583 AC: 2999 AN: 5146

South Asian (SAS) AF: 0.575 AC: 2767 AN: 4808

European-Finnish (FIN) AF: 0.656 AC: 6926 AN: 10556

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47162 AN: 67986

Other (OTH) AF: 0.627 AC: 1325 AN: 2114

Alfa AF: 0.654 Hom.: 4276

Bravo AF: 0.618

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.65
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs580859; hg19: chr13-69132440;