Genetic Variant LINC00243:n.693G>A (chr6-30814225-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 ENST00000399196.1(LINC00243):n.693G>A 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 0.0828 in 456,016 control chromosomes in the GnomAD database, including 2,309 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 0.085 ( 707 hom., cov: 32)

Exomes 𝑓: 0.082 ( 1602 hom. )

Consequence

LINC00243
ENST00000399196.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459

Publications

67 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1 link	n.693G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00243	ENST00000399196.1 link	n.693G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00243	ENST00000719498.1 link	n.896G>A	non_coding_transcript_exon_variant	Exon 2 of 2
LINC00243	ENST00000719499.1 link	n.610G>A	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0849

AC:

12912

AN:

152130

Hom.:

707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0590

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.0416

Gnomad ASJ

AF:

0.0629

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0170

Gnomad FIN

AF:

0.0698

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.0735

GnomAD2 exomes

AF:

0.0708

AC:

9693

AN:

136982

AF XY:

0.0712

show subpopulations

Gnomad AFR exome

AF:

0.0610

Gnomad AMR exome

AF:

0.0303

Gnomad ASJ exome

AF:

0.0619

Gnomad EAS exome

AF:

0.000286

Gnomad FIN exome

AF:

0.0721

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.0794

GnomAD4 exome

AF:

0.0818

AC:

24840

AN:

303768

Hom.:

1602

Cov.:

AF XY:

0.0763

AC XY:

13209

AN XY:

173024

show subpopulations

African (AFR)

AF:

0.0599

AC:

516

AN:

8608

American (AMR)

AF:

0.0303

AC:

825

AN:

27240

Ashkenazi Jewish (ASJ)

AF:

0.0652

AC:

696

AN:

10678

East Asian (EAS)

AF:

0.000434

AC:

AN:

9210

South Asian (SAS)

AF:

0.0200

AC:

1191

AN:

59600

European-Finnish (FIN)

AF:

0.0814

AC:

1046

AN:

12850

Middle Eastern (MID)

AF:

0.0814

AC:

226

AN:

2778

European-Non Finnish (NFE)

AF:

0.120

AC:

19085

AN:

158536

Other (OTH)

AF:

0.0877

AC:

1251

AN:

14268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1383

2766

4148

5531

6914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

216

288

360

<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:

0.0848

AC:

12905

AN:

152248

Hom.:

707

Cov.:

AF XY:

0.0783

AC XY:

5827

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0588

AC:

2445

AN:

41558

American (AMR)

AF:

0.0414

AC:

634

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0629

AC:

218

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5184

South Asian (SAS)

AF:

0.0166

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0698

AC:

741

AN:

10614

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8477

AN:

67980

Other (OTH)

AF:

0.0728

AC:

154

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

598

1195

1793

2390

2988

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.111

Hom.:

4967

Bravo

AF:

0.0826

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.76

(source)

DANN

Benign

0.55

PhyloP100

-0.46

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

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