Genetic Variant LINC01340:n.277+25589T>C (chr5-97696273-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 ENST00000715761.1(LINC01340):n.277+25589T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,186 control chromosomes in the GnomAD database, including 445 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 0.049 ( 445 hom., cov: 32)

Consequence

LINC01340
ENST00000715761.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.683

Publications

0 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=-0.66).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 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+25589T>C	intron_variant	Intron 3 of 6
LINC01340	ENST00000746238.1 link	n.382+25589T>C	intron_variant	Intron 4 of 8
LINC01340	ENST00000746239.1 link	n.362+25589T>C	intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes

AF:

0.0489

AC:

7430

AN:

152068

Hom.:

440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0371

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.0902

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.0316

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00390

Gnomad OTH

AF:

0.0439

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

GnomAD4 genome

AF:

0.0491

AC:

7465

AN:

152186

Hom.:

445

Cov.:

AF XY:

0.0496

AC XY:

3692

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.135

AC:

5609

AN:

41530

American (AMR)

AF:

0.0370

AC:

565

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3468

East Asian (EAS)

AF:

0.0900

AC:

465

AN:

5166

South Asian (SAS)

AF:

0.0180

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0316

AC:

335

AN:

10612

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00390

AC:

265

AN:

68012

Other (OTH)

AF:

0.0458

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

333

667

1000

1334

1667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0174

Hom.:

133

Bravo

AF:

0.0546

Asia WGS

AF:

0.0620

AC:

216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

(source)

DANN

Benign

0.42

PhyloP100

0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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