Genetic Variant LINC00243:n.146-2724A>G (chr6-30817496-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 ENST00000399196.1(LINC00243):n.146-2724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,238 control chromosomes in the GnomAD database, including 3,107 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 0.18 ( 3107 hom., cov: 32)

Consequence

LINC00243
ENST00000399196.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.419

Publications

32 publications found

Variant links:

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

LINC00243 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1 link	n.146-2724A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00243	ENST00000399196.1 link	n.146-2724A>G	intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.7 link	n.145+13019A>G	intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1 link	n.128-2724A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27223

AN:

152120

Hom.:

3102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0961

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.204

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

GnomAD4 genome

AF:

0.179

AC:

27252

AN:

152238

Hom.:

3107

Cov.:

AF XY:

0.187

AC XY:

13924

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0963

AC:

4000

AN:

41546

American (AMR)

AF:

0.306

AC:

4671

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1116

AN:

3468

East Asian (EAS)

AF:

0.436

AC:

2261

AN:

5180

South Asian (SAS)

AF:

0.380

AC:

1833

AN:

4826

European-Finnish (FIN)

AF:

0.155

AC:

1644

AN:

10610

Middle Eastern (MID)

AF:

0.212

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.162

AC:

10987

AN:

68012

Other (OTH)

AF:

0.205

AC:

434

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1090

2181

3271

4362

5452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.176

Hom.:

11091

Bravo

AF:

0.186

Asia WGS

AF:

0.393

AC:

1367

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

0.42

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