XR_007063845.1:n.-184A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370324	XR_007063845.1	n.-184A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;