chr11-130659324-A-G

Variant names:

• chr11-130659324-A-G
• rs12792526
• ENST00000721900.1:n.193+27843A>G

Variant summary

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

The ENST00000721900.1(LINC02873):​n.193+27843A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,836 control chromosomes in the GnomAD database, including 2,109 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 0.14 (2109 hom., cov: 31)
• Consequence: LINC02873 ENST00000721900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 2 publications found

Genes affected

LINC02873 (HGNC:26805): (long intergenic non-protein coding RNA 2873)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721900.1. You can select a different transcript below to see updated ACMG assignments.

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
	LINC02873	ENST00000721900.1		n.193+27843A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21388 AN: 151718 Hom.: 2114 Cov.: 31

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.141 AC: 21376 AN: 151836 Hom.: 2109 Cov.: 31 AF XY: 0.148 AC XY: 10954 AN XY: 74200

African (AFR) AF: 0.0446 AC: 1851 AN: 41492

American (AMR) AF: 0.311 AC: 4732 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3460

East Asian (EAS) AF: 0.329 AC: 1689 AN: 5134

South Asian (SAS) AF: 0.162 AC: 774 AN: 4784

European-Finnish (FIN) AF: 0.180 AC: 1884 AN: 10478

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9275 AN: 67936

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.150 Hom.: 1809

Bravo AF: 0.146

Asia WGS AF: 0.261 AC: 904 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12792526;

hg19: chr11-130529219;