chr15-47821746-C-T

Variant names:

• chr15-47821746-C-T
• rs963031
• ENST00000558434.2:n.307-1589G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000558434.2(LINC01491):​n.307-1589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,100 control chromosomes in the GnomAD database, including 495 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 0.070 (495 hom., cov: 32)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.097 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.282+5825G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558434.2	n.307-1589G>A		intron_variant	Intron 3 of 4	3
LINC01491	ENST00000558792.6	n.308+5813G>A		intron_variant	Intron 3 of 6	3
LINC01491	ENST00000561238.3	n.330+5813G>A		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10652 AN: 151982 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0700 AC: 10641 AN: 152100 Hom.: 495 Cov.: 32 AF XY: 0.0688 AC XY: 5114 AN XY: 74344

African (AFR) AF: 0.0216 AC: 897 AN: 41502

American (AMR) AF: 0.0648 AC: 990 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.0519 AC: 268 AN: 5162

South Asian (SAS) AF: 0.0910 AC: 438 AN: 4812

European-Finnish (FIN) AF: 0.0700 AC: 740 AN: 10576

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 290

European-Non Finnish (NFE) AF: 0.0990 AC: 6731 AN: 67990

Other (OTH) AF: 0.0815 AC: 172 AN: 2110

Alfa AF: 0.0885 Hom.: 980

Bravo AF: 0.0692

Asia WGS AF: 0.0910 AC: 318 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs963031; hg19: chr15-48113943;