Genetic Variant LINC01149:n.414A>G (chr6-31442080-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430364.1(LINC01149):n.414A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,724 control chromosomes in the GnomAD database, including 4,267 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 0.22 ( 4265 hom., cov: 30)

Exomes 𝑓: 0.19 ( 2 hom. )

Consequence

LINC01149
ENST00000430364.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460

Publications

11 publications found

Variant links:

Genes affected

LINC01149 (HGNC:39757): (long intergenic non-protein coding RNA 1149)

LINC01149 links:

ENSG00000288587 (HGNC:):

ENSG00000288587 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01149	NR_144465.1 link	n.414A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01149	ENST00000430364.1 link	n.414A>G	non_coding_transcript_exon_variant	Exon 1 of 2	1
LINC01149	ENST00000812003.1 link	n.438A>G	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000288587	ENST00000673857.1 link	n.63-21043A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32825

AN:

151470

Hom.:

4257

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.205

GnomAD4 exome

AF:

0.188

AC:

AN:

138

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.174

AC:

AN:

Other (OTH)

AF:

0.143

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.217

AC:

32870

AN:

151586

Hom.:

4265

Cov.:

AF XY:

0.222

AC XY:

16435

AN XY:

74092

show subpopulations

African (AFR)

AF:

0.314

AC:

12937

AN:

41180

American (AMR)

AF:

0.269

AC:

4086

AN:

15166

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

955

AN:

3470

East Asian (EAS)

AF:

0.182

AC:

933

AN:

5128

South Asian (SAS)

AF:

0.229

AC:

1099

AN:

4806

European-Finnish (FIN)

AF:

0.232

AC:

2453

AN:

10562

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9597

AN:

67976

Other (OTH)

AF:

0.204

AC:

427

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1249

2498

3747

4996

6245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.168

Hom.:

2425

Bravo

AF:

0.222

Asia WGS

AF:

0.200

AC:

692

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.2

(source)

DANN

Benign

0.44

PhyloP100

-0.046

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over