ENST00000512487.2:n.526-24112A>G

Variant names:

• chr4-181088592-T-C
• rs7689941
• ENST00000512487.2:n.526-24112A>G

Variant summary

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

The ENST00000512487.2(LINC00290):​n.526-24112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,042 control chromosomes in the GnomAD database, including 19,325 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 0.47 (19325 hom., cov: 31)
• Consequence: LINC00290 ENST00000512487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 2 publications found

Genes affected

LINC00290 (HGNC:38515): (long intergenic non-protein coding RNA 290)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512487.2. 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
	LINC00290	NR_033918.1		n.202-24112A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00290	ENST00000512487.2	TSL:1	n.526-24112A>G		intron	N/A
	LINC00290	ENST00000778348.1		n.288-24112A>G		intron	N/A
	LINC00290	ENST00000778349.1		n.236-24112A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71910 AN: 151924 Hom.: 19325 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.473 AC: 71914 AN: 152042 Hom.: 19325 Cov.: 31 AF XY: 0.474 AC XY: 35251 AN XY: 74312

African (AFR) AF: 0.206 AC: 8537 AN: 41472

American (AMR) AF: 0.585 AC: 8930 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3726 AN: 5156

South Asian (SAS) AF: 0.463 AC: 2231 AN: 4814

European-Finnish (FIN) AF: 0.542 AC: 5721 AN: 10554

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38839 AN: 67980

Other (OTH) AF: 0.535 AC: 1132 AN: 2116

Alfa AF: 0.538 Hom.: 15878

Bravo AF: 0.470

Asia WGS AF: 0.565 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs7689941; hg19: chr4-182009745;