rs9586843

Variant names:

• chr13-105393985-C-T
• rs9586843

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 0.259 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.369 AC: 15299 AN: 41422

American (AMR) AF: 0.302 AC: 4599 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1430 AN: 5142

South Asian (SAS) AF: 0.192 AC: 927 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2843 AN: 10546

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12889 AN: 67962

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.234 Hom.: 1773

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9586843; hg19: chr13-106046335;