rs1025759

Variant names:

• chr15-47776253-T-G
• rs1025759
• ENST00000558792.6:n.572-1845A>C

Variant summary

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

The ENST00000558792.6(LINC01491):​n.572-1845A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,110 control chromosomes in the GnomAD database, including 1,520 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 0.12 (1520 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.572-1845A>C		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.580-1845A>C		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.620-1845A>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17711 AN: 151992 Hom.: 1517 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17739 AN: 152110 Hom.: 1520 Cov.: 32 AF XY: 0.121 AC XY: 8964 AN XY: 74362

African (AFR) AF: 0.163 AC: 6745 AN: 41492

American (AMR) AF: 0.180 AC: 2755 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2226 AN: 5144

South Asian (SAS) AF: 0.0800 AC: 385 AN: 4810

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0589 AC: 4006 AN: 67998

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.101 Hom.: 212

Bravo AF: 0.132

Asia WGS AF: 0.200 AC: 696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1025759; hg19: chr15-48068450;