rs9586149

Variant names:

• chr13-87970485-C-T
• rs9586149

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 0.0845 in 151,816 control chromosomes in the GnomAD database, including 735 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 0.084 (735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0844 AC: 12805 AN: 151700 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0845 AC: 12824 AN: 151816 Hom.: 735 Cov.: 32 AF XY: 0.0849 AC XY: 6295 AN XY: 74182

African (AFR) AF: 0.163 AC: 6747 AN: 41410

American (AMR) AF: 0.0507 AC: 773 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5178

South Asian (SAS) AF: 0.0567 AC: 273 AN: 4814

European-Finnish (FIN) AF: 0.0923 AC: 969 AN: 10500

Middle Eastern (MID) AF: 0.0897 AC: 26 AN: 290

European-Non Finnish (NFE) AF: 0.0511 AC: 3468 AN: 67892

Other (OTH) AF: 0.0684 AC: 144 AN: 2106

Alfa AF: 0.0620 Hom.: 1197

Bravo AF: 0.0837

Asia WGS AF: 0.0330 AC: 115 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.37
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs9586149; hg19: chr13-88622740;