rs13202860

Variant names:

• chr6-86445536-A-T
• rs13202860

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 0.0681 in 152,300 control chromosomes in the GnomAD database, including 478 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 0.068 (478 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10366 AN: 152182 Hom.: 479 Cov.: 33

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.0916

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

GnomAD4 genome AF: 0.0681 AC: 10365 AN: 152300 Hom.: 478 Cov.: 33 AF XY: 0.0689 AC XY: 5129 AN XY: 74476

African (AFR) AF: 0.0188 AC: 781 AN: 41580

American (AMR) AF: 0.0811 AC: 1241 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3470

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5184

South Asian (SAS) AF: 0.137 AC: 663 AN: 4826

European-Finnish (FIN) AF: 0.0745 AC: 791 AN: 10616

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5886 AN: 68016

Other (OTH) AF: 0.0892 AC: 188 AN: 2108

Alfa AF: 0.0818 Hom.: 298

Bravo AF: 0.0642

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.48
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs13202860; hg19: chr6-87155254;