Genetic Variant LINC01465:n.291A>G (chr12-62603400-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 ENST00000408887.3(LINC01465):n.291A>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 0.412 in 1,189,168 control chromosomes in the GnomAD database, including 101,417 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 0.42 ( 13471 hom., cov: 32)

Exomes 𝑓: 0.41 ( 87946 hom. )

Consequence

LINC01465
ENST00000408887.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574

Publications

49 publications found

Variant links:

Genes affected

LINC01465 (HGNC:26364): (long intergenic non-protein coding RNA 1465)

LINC01465 links:

ENSG00000275180 (HGNC:):

ENSG00000275180 links:

MIRLET7IHG (HGNC:55478): (MIRLET7I host gene)

MIRLET7IHG 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01465	NR_121682.1 link	n.35A>G		non_coding_transcript_exon_variant	Exon 1 of 1
MIRLET7IHG	NR_186001.1 link	n.93+565T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01465	ENST00000408887.3 link	n.291A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000275180	ENST00000619323.3 link	n.208T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIRLET7IHG	ENST00000550290.2 link	n.84+565T>C	intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63409

AN:

151790

Hom.:

13463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.423

GnomAD4 exome

AF:

0.411

AC:

426123

AN:

1037262

Hom.:

87946

Cov.:

AF XY:

0.411

AC XY:

205462

AN XY:

500336

show subpopulations

African (AFR)

AF:

0.477

AC:

8753

AN:

18358

American (AMR)

AF:

0.343

AC:

4627

AN:

13482

Ashkenazi Jewish (ASJ)

AF:

0.501

AC:

4751

AN:

9486

East Asian (EAS)

AF:

0.356

AC:

3328

AN:

9348

South Asian (SAS)

AF:

0.392

AC:

24273

AN:

61906

European-Finnish (FIN)

AF:

0.362

AC:

5023

AN:

13890

Middle Eastern (MID)

AF:

0.442

AC:

1020

AN:

2310

European-Non Finnish (NFE)

AF:

0.412

AC:

358996

AN:

871696

Other (OTH)

AF:

0.417

AC:

15352

AN:

36786

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

12417

24835

37252

49670

62087

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13484

26968

40452

53936

67420

<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:

0.418

AC:

63441

AN:

151906

Hom.:

13471

Cov.:

AF XY:

0.413

AC XY:

30684

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.481

AC:

19920

AN:

41418

American (AMR)

AF:

0.370

AC:

5663

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

1741

AN:

3468

East Asian (EAS)

AF:

0.347

AC:

1774

AN:

5108

South Asian (SAS)

AF:

0.389

AC:

1878

AN:

4822

European-Finnish (FIN)

AF:

0.377

AC:

3987

AN:

10570

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.400

AC:

27151

AN:

67910

Other (OTH)

AF:

0.418

AC:

883

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1930

3861

5791

7722

9652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<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:

0.402

Hom.:

1566

Bravo

AF:

0.421

Asia WGS

AF:

0.330

AC:

1143

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.8

(source)

DANN

Benign

0.33

PhyloP100

-0.57

Mutation Taster

=300/0

polymorphism (auto)

(source)

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