rs13202860

Positions:

• chr6-86445536-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 0.0681 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0351

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0745

Gnomad4 NFE AF: 0.0865

Gnomad4 OTH AF: 0.0892

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13202860; hg19: chr6-87155254;