ENST00000558434.2:n.306+3371A>G

Variant names:

• chr15-47824200-T-C
• rs494230
• ENST00000558434.2:n.306+3371A>G

Variant summary

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

The ENST00000558434.2(LINC01491):​n.306+3371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,094 control chromosomes in the GnomAD database, including 21,976 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 0.49 (21976 hom., cov: 33)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 0 publications found

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558434.2. 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
	LINC01491	NR_120336.1		n.282+3371A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558434.2	TSL:3	n.306+3371A>G		intron	N/A
	LINC01491	ENST00000558792.6	TSL:3	n.308+3359A>G		intron	N/A
	LINC01491	ENST00000561238.3	TSL:3	n.330+3359A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73719 AN: 151976 Hom.: 21921 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.485 AC: 73837 AN: 152094 Hom.: 21976 Cov.: 33 AF XY: 0.486 AC XY: 36162 AN XY: 74350

African (AFR) AF: 0.827 AC: 34329 AN: 41512

American (AMR) AF: 0.453 AC: 6924 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3464

East Asian (EAS) AF: 0.716 AC: 3701 AN: 5168

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4814

European-Finnish (FIN) AF: 0.355 AC: 3757 AN: 10570

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20571 AN: 67966

Other (OTH) AF: 0.450 AC: 952 AN: 2114

Alfa AF: 0.404 Hom.: 12165

Bravo AF: 0.513

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.43
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs494230; hg19: chr15-48116397;