15-47843367-C-T

Variant names:

• chr15-47843367-C-T
• rs785016
• ENST00000558434.2:n.260+1471G>A

Variant summary

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

The ENST00000558434.2(LINC01491):​n.260+1471G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,022 control chromosomes in the GnomAD database, including 21,458 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 0.52 (21458 hom., cov: 33)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.236+1471G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558434.2	n.260+1471G>A		intron_variant	Intron 2 of 4	3
LINC01491	ENST00000558792.6	n.250+1471G>A		intron_variant	Intron 2 of 6	3
LINC01491	ENST00000561238.3	n.272+1471G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78793 AN: 151902 Hom.: 21416 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.519 AC: 78892 AN: 152022 Hom.: 21458 Cov.: 33 AF XY: 0.523 AC XY: 38863 AN XY: 74274

African (AFR) AF: 0.664 AC: 27554 AN: 41474

American (AMR) AF: 0.556 AC: 8491 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3552 AN: 5160

South Asian (SAS) AF: 0.535 AC: 2582 AN: 4826

European-Finnish (FIN) AF: 0.463 AC: 4876 AN: 10522

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28947 AN: 67972

Other (OTH) AF: 0.522 AC: 1105 AN: 2116

Alfa AF: 0.463 Hom.: 37862

Bravo AF: 0.532

Asia WGS AF: 0.681 AC: 2367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs785016; hg19: chr15-48135564;