Genetic Variant LINC01395:n.818T>C (chr11-129612280-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 ENST00000631195.1(LINC01395):n.818T>C 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 0.701 in 151,992 control chromosomes in the GnomAD database, including 37,458 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 0.70 ( 37455 hom., cov: 31)

Exomes 𝑓: 0.67 ( 3 hom. )

Consequence

LINC01395
ENST00000631195.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Publications

5 publications found

Variant links:

Genes affected

LINC01395 (HGNC:50674): (long intergenic non-protein coding RNA 1395)

LINC01395 links:

ENSG00000281386 (HGNC:):

ENSG00000281386 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01395	NR_120582.1 link	n.818T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01395	ENST00000631195.1 link	n.818T>C		non_coding_transcript_exon_variant	Exon 4 of 4	1
ENSG00000281386	ENST00000626400.2 link	n.699A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106431

AN:

151862

Hom.:

37445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.599

Gnomad AMR

AF:

0.745

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.804

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.803

Gnomad NFE

AF:

0.719

Gnomad OTH

AF:

0.716

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.800

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.701

AC:

106483

AN:

151980

Hom.:

37455

Cov.:

AF XY:

0.702

AC XY:

52137

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.643

AC:

26635

AN:

41436

American (AMR)

AF:

0.745

AC:

11380

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

2407

AN:

3472

East Asian (EAS)

AF:

0.778

AC:

4017

AN:

5162

South Asian (SAS)

AF:

0.805

AC:

3879

AN:

4820

European-Finnish (FIN)

AF:

0.663

AC:

6989

AN:

10538

Middle Eastern (MID)

AF:

0.788

AC:

230

AN:

292

European-Non Finnish (NFE)

AF:

0.719

AC:

48893

AN:

67968

Other (OTH)

AF:

0.715

AC:

1508

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1618

3236

4855

6473

8091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.720

Hom.:

65758

Bravo

AF:

0.703

Asia WGS

AF:

0.788

AC:

2739

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.0

(source)

DANN

Benign

0.51

PhyloP100

1.0

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