11-45792030-G-C

Variant names:

• chr11-45792030-G-C
• rs12285276
• ENST00000811651.1:n.157+1574C>G

Variant summary

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

The ENST00000811651.1(LINC02690):​n.157+1574C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,026 control chromosomes in the GnomAD database, including 12,949 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 0.38 (12949 hom., cov: 32)
• Consequence: LINC02690 ENST00000811651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 9 publications found

Genes affected

LINC02690 (HGNC:54194): (long intergenic non-protein coding RNA 2690)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02690	ENST00000811651.1		n.157+1574C>G		intron	N/A
	LINC02690	ENST00000811652.1		n.271+1574C>G		intron	N/A
	LINC02690	ENST00000811653.1		n.158+1574C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56952 AN: 151908 Hom.: 12918 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.375 AC: 57038 AN: 152026 Hom.: 12949 Cov.: 32 AF XY: 0.378 AC XY: 28071 AN XY: 74312

African (AFR) AF: 0.622 AC: 25767 AN: 41436

American (AMR) AF: 0.343 AC: 5247 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3180 AN: 5174

South Asian (SAS) AF: 0.304 AC: 1461 AN: 4804

European-Finnish (FIN) AF: 0.319 AC: 3371 AN: 10578

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16274 AN: 67950

Other (OTH) AF: 0.352 AC: 744 AN: 2116

Alfa AF: 0.243 Hom.: 2882

Bravo AF: 0.388

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12285276; hg19: chr11-45813581;