Genetic Variant LINC01091:n.546-40455C>A (chr4-123612332-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000662928.1(LINC01091):n.546-40455C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,100 control chromosomes in the GnomAD database, including 1,749 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 0.13 ( 1749 hom., cov: 32)

Consequence

LINC01091
ENST00000662928.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

2 publications found

Variant links:

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

LINC01091 links:

ENSG00000304190 (HGNC:):

ENSG00000304190 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01091	ENST00000662928.1 link	n.546-40455C>A	intron_variant	Intron 1 of 3
LINC01091	ENST00000664622.1 link	n.212-40459C>A	intron_variant	Intron 1 of 8
LINC01091	ENST00000666328.1 link	n.637-40455C>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20395

AN:

151982

Hom.:

1752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0318

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.128

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

GnomAD4 genome

AF:

0.134

AC:

20396

AN:

152100

Hom.:

1749

Cov.:

AF XY:

0.140

AC XY:

10385

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0320

AC:

1328

AN:

41522

American (AMR)

AF:

0.157

AC:

2404

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

388

AN:

3468

East Asian (EAS)

AF:

0.167

AC:

861

AN:

5158

South Asian (SAS)

AF:

0.203

AC:

977

AN:

4814

European-Finnish (FIN)

AF:

0.240

AC:

2536

AN:

10562

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11451

AN:

67984

Other (OTH)

AF:

0.126

AC:

266

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

865

1730

2595

3460

4325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.155

Hom.:

1050

Bravo

AF:

0.120

Asia WGS

AF:

0.162

AC:

563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.63

(source)

DANN

Benign

0.23

PhyloP100

-0.49

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