Genetic Variant LINC01491:n.415-877C>G (chr15-47805755-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000558792.6(LINC01491):n.415-877C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,108 control chromosomes in the GnomAD database, including 3,434 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 0.20 ( 3434 hom., cov: 32)

Consequence

LINC01491
ENST00000558792.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.469

Publications

2 publications found

Variant links:

Genes affected

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

LINC01491 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1 link	n.283-877C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01491	ENST00000558792.6 link	n.415-877C>G	intron_variant	Intron 4 of 6	3
LINC01491	ENST00000651940.1 link	n.279-877C>G	intron_variant	Intron 3 of 6
LINC01491	ENST00000653152.1 link	n.319-877C>G	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29813

AN:

151990

Hom.:

3434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0639

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.225

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

GnomAD4 genome

AF:

0.196

AC:

29827

AN:

152108

Hom.:

3434

Cov.:

AF XY:

0.201

AC XY:

14948

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.0639

AC:

2654

AN:

41512

American (AMR)

AF:

0.227

AC:

3465

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

838

AN:

3470

East Asian (EAS)

AF:

0.179

AC:

927

AN:

5168

South Asian (SAS)

AF:

0.218

AC:

1050

AN:

4826

European-Finnish (FIN)

AF:

0.300

AC:

3165

AN:

10554

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.249

AC:

16946

AN:

67980

Other (OTH)

AF:

0.222

AC:

470

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1200

2399

3599

4798

5998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.208

Hom.:

442

Bravo

AF:

0.186

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.8

(source)

DANN

Benign

0.65

PhyloP100

0.47

Splicing

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

Publications

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15-47805755-G-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over