15-47829115-G-C

Variant names:

• chr15-47829115-G-C
• rs530734
• ENST00000558434.2:n.261-1499C>G

Variant summary

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

The ENST00000558434.2(LINC01491):​n.261-1499C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,108 control chromosomes in the GnomAD database, including 2,276 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 (2276 hom., cov: 32)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	NR_120336.1		n.237-1499C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558434.2	TSL:3	n.261-1499C>G		intron	N/A
	LINC01491	ENST00000558792.6	TSL:3	n.251-1499C>G		intron	N/A
	LINC01491	ENST00000561238.3	TSL:3	n.273-1499C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17927 AN: 151990 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0429

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.118 AC: 17974 AN: 152108 Hom.: 2276 Cov.: 32 AF XY: 0.119 AC XY: 8843 AN XY: 74356

African (AFR) AF: 0.310 AC: 12825 AN: 41436

American (AMR) AF: 0.111 AC: 1700 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3470

East Asian (EAS) AF: 0.185 AC: 958 AN: 5170

South Asian (SAS) AF: 0.0741 AC: 357 AN: 4818

European-Finnish (FIN) AF: 0.0429 AC: 454 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1374 AN: 68020

Other (OTH) AF: 0.100 AC: 211 AN: 2110

Alfa AF: 0.0246 Hom.: 42

Bravo AF: 0.132

Asia WGS AF: 0.166 AC: 576 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.33
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs530734;

hg19: chr15-48121312;