rs9584669

Variant names:

• chr13-97711228-T-C
• rs9584669
• XR_007063845.1:n.-184A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063845.1(LOC105370324):​n.-184A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,078 control chromosomes in the GnomAD database, including 3,365 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 0.18 (3365 hom., cov: 33)
• Consequence: LOC105370324 XR_007063845.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 7 publications found

Genes affected

LOC105370324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27476 AN: 151960 Hom.: 3357 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.181 AC: 27529 AN: 152078 Hom.: 3365 Cov.: 33 AF XY: 0.175 AC XY: 12986 AN XY: 74336

African (AFR) AF: 0.352 AC: 14607 AN: 41442

American (AMR) AF: 0.141 AC: 2151 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3466

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5186

South Asian (SAS) AF: 0.122 AC: 588 AN: 4822

European-Finnish (FIN) AF: 0.0595 AC: 630 AN: 10580

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8060 AN: 67984

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.138 Hom.: 915

Bravo AF: 0.195

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.36
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9584669; hg19: chr13-98363482;