rs9585170

Variant names:

• chr13-86392124-G-A
• rs9585170

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 0.211 in 151,864 control chromosomes in the GnomAD database, including 3,680 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 0.21 (3680 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 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: 0.211 AC: 32045 AN: 151746 Hom.: 3675 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.211 AC: 32065 AN: 151864 Hom.: 3680 Cov.: 33 AF XY: 0.205 AC XY: 15201 AN XY: 74222

African (AFR) AF: 0.269 AC: 11133 AN: 41418

American (AMR) AF: 0.169 AC: 2576 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3470

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5160

South Asian (SAS) AF: 0.121 AC: 582 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1620 AN: 10546

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14699 AN: 67910

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.211 Hom.: 1848

Bravo AF: 0.214

Asia WGS AF: 0.0650 AC: 227 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9585170; hg19: chr13-87044379;