Genetic Variant LINC01491:n.572-4270C>T (chr15-47778678-G-A) – 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.572-4270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,014 control chromosomes in the GnomAD database, including 5,541 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 0.27 ( 5541 hom., cov: 33)

Consequence

LINC01491
ENST00000558792.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.482

Publications

0 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01491	ENST00000558792.6 link	n.572-4270C>T	intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1 link	n.580-4270C>T	intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1 link	n.620-4270C>T	intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40339

AN:

151896

Hom.:

5539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.339

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.267

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

GnomAD4 genome

AF:

0.265

AC:

40355

AN:

152014

Hom.:

5541

Cov.:

AF XY:

0.266

AC XY:

19777

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.240

AC:

9938

AN:

41462

American (AMR)

AF:

0.231

AC:

3532

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

1162

AN:

3464

East Asian (EAS)

AF:

0.152

AC:

788

AN:

5180

South Asian (SAS)

AF:

0.260

AC:

1251

AN:

4818

European-Finnish (FIN)

AF:

0.339

AC:

3579

AN:

10546

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.285

AC:

19366

AN:

67960

Other (OTH)

AF:

0.266

AC:

561

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1535

3070

4605

6140

7675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.291

Hom.:

2314

Bravo

AF:

0.249

Asia WGS

AF:

0.241

AC:

838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.8

(source)

DANN

Benign

0.39

PhyloP100

0.48

Splicing

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

Publications

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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