Genetic Variant LINC01182:n.728-13156T>C (chr4-14049108-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715489.1(LINC01182):n.728-13156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,192 control chromosomes in the GnomAD database, including 63,792 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 0.91 ( 63792 hom., cov: 32)

Consequence

LINC01182
ENST00000715489.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

3 publications found

Variant links:

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

LINC01182 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 (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01182	ENST00000715489.1 link	n.728-13156T>C	intron_variant	Intron 5 of 8
LINC01182	ENST00000715490.1 link	n.342+12672T>C	intron_variant	Intron 2 of 3
LINC01182	ENST00000715491.1 link	n.183-13156T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.915

AC:

139126

AN:

152074

Hom.:

63734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.950

Gnomad AMI

AF:

0.944

Gnomad AMR

AF:

0.958

Gnomad ASJ

AF:

0.922

Gnomad EAS

AF:

0.967

Gnomad SAS

AF:

0.916

Gnomad FIN

AF:

0.856

Gnomad MID

AF:

0.930

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.933

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

GnomAD4 genome

AF:

0.915

AC:

139241

AN:

152192

Hom.:

63792

Cov.:

AF XY:

0.914

AC XY:

68041

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.950

AC:

39450

AN:

41548

American (AMR)

AF:

0.958

AC:

14620

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.922

AC:

3200

AN:

3472

East Asian (EAS)

AF:

0.968

AC:

5006

AN:

5174

South Asian (SAS)

AF:

0.916

AC:

4416

AN:

4822

European-Finnish (FIN)

AF:

0.856

AC:

9082

AN:

10606

Middle Eastern (MID)

AF:

0.935

AC:

275

AN:

294

European-Non Finnish (NFE)

AF:

0.888

AC:

60356

AN:

67986

Other (OTH)

AF:

0.934

AC:

1975

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

636

1272

1908

2544

3180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.898

Hom.:

33144

Bravo

AF:

0.925

Asia WGS

AF:

0.949

AC:

3295

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.32

(source)

DANN

Benign

0.51

PhyloP100

-1.4

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