13-99432879-T-C

Variant names:

• chr13-99432879-T-C
• rs9517725
• ENST00000646895.1:n.-177A>G

Variant summary

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

The ENST00000646895.1(LNCARGI):​n.-177A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,216 control chromosomes in the GnomAD database, including 51,117 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 0.81 (51117 hom., cov: 34)
• Consequence: LNCARGI ENST00000646895.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 5 publications found

Genes affected

LNCARGI (HGNC:56890):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCARGI	NR_197584.1	n.-129A>G		upstream_gene_variant
LNCARGI	NR_197585.1	n.-129A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCARGI	ENST00000646895.1	n.-177A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123344 AN: 152098 Hom.: 51090 Cov.: 34

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.811 AC: 123425 AN: 152216 Hom.: 51117 Cov.: 34 AF XY: 0.811 AC XY: 60363 AN XY: 74414

African (AFR) AF: 0.619 AC: 25683 AN: 41512

American (AMR) AF: 0.889 AC: 13597 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3035 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4604 AN: 5166

South Asian (SAS) AF: 0.798 AC: 3851 AN: 4828

European-Finnish (FIN) AF: 0.858 AC: 9100 AN: 10604

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60699 AN: 68016

Other (OTH) AF: 0.826 AC: 1743 AN: 2110

Alfa AF: 0.860 Hom.: 150153

Bravo AF: 0.809

Asia WGS AF: 0.832 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs9517725; hg19: chr13-100085133;