Genetic Variant LINC01340:n.277+66431C>T (chr5-97737115-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 ENST00000715761.1(LINC01340):n.277+66431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,756 control chromosomes in the GnomAD database, including 1,260 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 0.11 ( 1260 hom., cov: 32)

Consequence

LINC01340
ENST00000715761.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.651

Publications

2 publications found

Variant links:

Genes affected

LINC01340 (HGNC:50550): (long intergenic non-protein coding RNA 1340)

LINC01340 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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01340	ENST00000715761.1 link	n.277+66431C>T	intron_variant	Intron 3 of 6
LINC01340	ENST00000746238.1 link	n.382+66431C>T	intron_variant	Intron 4 of 8
LINC01340	ENST00000746239.1 link	n.362+66431C>T	intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16712

AN:

151638

Hom.:

1259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.135

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.0661

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0996

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.110

AC:

16727

AN:

151756

Hom.:

1260

Cov.:

AF XY:

0.111

AC XY:

8213

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.115

AC:

4784

AN:

41468

American (AMR)

AF:

0.109

AC:

1657

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

468

AN:

3466

East Asian (EAS)

AF:

0.174

AC:

902

AN:

5180

South Asian (SAS)

AF:

0.226

AC:

1085

AN:

4808

European-Finnish (FIN)

AF:

0.0661

AC:

694

AN:

10506

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0995

AC:

6745

AN:

67776

Other (OTH)

AF:

0.118

AC:

249

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

755

1510

2265

3020

3775

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.113

Hom.:

711

Bravo

AF:

0.108

Asia WGS

AF:

0.213

AC:

744

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.49

(source)

DANN

Benign

0.31

PhyloP100

-0.65

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