Genetic Variant LINC01370:n.309-3667C>T (chr20-40027058-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000423153.2(LINC01370):n.309-3667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,070 control chromosomes in the GnomAD database, including 21,607 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 0.50 ( 21607 hom., cov: 32)

Consequence

LINC01370
ENST00000423153.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450

Publications

2 publications found

Variant links:

Genes affected

LINC01370 (HGNC:50608): (long intergenic non-protein coding RNA 1370)

LINC01370 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 (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01370	ENST00000423153.2 link	n.309-3667C>T	intron_variant	Intron 2 of 5	3
LINC01370	ENST00000716850.1 link	n.309-7103C>T	intron_variant	Intron 2 of 3
LINC01370	ENST00000722236.1 link	n.309-3667C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75899

AN:

151952

Hom.:

21606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.591

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.571

Gnomad SAS

AF:

0.476

Gnomad FIN

AF:

0.646

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.631

Gnomad OTH

AF:

0.493

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

GnomAD4 genome

AF:

0.499

AC:

75895

AN:

152070

Hom.:

21607

Cov.:

AF XY:

0.499

AC XY:

37090

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.219

AC:

9102

AN:

41508

American (AMR)

AF:

0.562

AC:

8589

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.442

AC:

1535

AN:

3470

East Asian (EAS)

AF:

0.571

AC:

2945

AN:

5156

South Asian (SAS)

AF:

0.476

AC:

2291

AN:

4818

European-Finnish (FIN)

AF:

0.646

AC:

6819

AN:

10562

Middle Eastern (MID)

AF:

0.476

AC:

140

AN:

294

European-Non Finnish (NFE)

AF:

0.631

AC:

42905

AN:

67968

Other (OTH)

AF:

0.488

AC:

1030

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1727

3455

5182

6910

8637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

662

1324

1986

2648

3310

<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:

0.582

Hom.:

44925

Bravo

AF:

0.480

Asia WGS

AF:

0.508

AC:

1767

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

DANN

Benign

0.44

PhyloP100

-0.045

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