rs9586843

Variant names:

• chr13-105393985-C-T
• rs9586843

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 0.259 in 151,918 control chromosomes in the GnomAD database, including 5,556 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 0.26 (5556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.259 AC: 39244 AN: 151800 Hom.: 5539 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.259 AC: 39298 AN: 151918 Hom.: 5556 Cov.: 31 AF XY: 0.262 AC XY: 19468 AN XY: 74240

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.242

Alfa AF: 0.235 Hom.: 1053

Bravo AF: 0.268

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9586843; hg19: chr13-106046335;