Genetic Variant LINC00652:n.70G>A (chr20-18794220-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 ENST00000454749.1(LINC00652):n.70G>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 0.132 in 152,164 control chromosomes in the GnomAD database, including 1,446 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 0.13 ( 1446 hom., cov: 32)

Exomes 𝑓: 0.086 ( 0 hom. )

Consequence

LINC00652
ENST00000454749.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.203

Publications

2 publications found

Variant links:

Genes affected

LINC00652 (HGNC:25003): (long intergenic non-protein coding RNA 652)

LINC00652 links:

LCDR (HGNC:44308): (lysosome cell death regulator)

LCDR 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00652	NR_026883.1 link	n.365G>A	non_coding_transcript_exon_variant	Exon 1 of 4
LCDR	NR_026885.1 link	n.172C>T	non_coding_transcript_exon_variant	Exon 1 of 1
LINC00652	NR_026884.1 link	n.-238G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00652	ENST00000454749.1 link	n.70G>A	non_coding_transcript_exon_variant	Exon 1 of 5	1
LINC00652	ENST00000455340.6 link	n.103G>A	non_coding_transcript_exon_variant	Exon 1 of 5	2
LCDR	ENST00000609087.2 link	n.143C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20136

AN:

151976

Hom.:

1446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0211

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.0857

AC:

AN:

Hom.:

Cov.:

AF XY:

0.109

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0800

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.417

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.132

AC:

20141

AN:

152094

Hom.:

1446

Cov.:

AF XY:

0.130

AC XY:

9701

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.103

AC:

4292

AN:

41510

American (AMR)

AF:

0.118

AC:

1810

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

380

AN:

3466

East Asian (EAS)

AF:

0.0208

AC:

107

AN:

5152

South Asian (SAS)

AF:

0.117

AC:

563

AN:

4826

European-Finnish (FIN)

AF:

0.159

AC:

1681

AN:

10584

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10870

AN:

67954

Other (OTH)

AF:

0.129

AC:

272

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

895

1790

2685

3580

4475

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.139

Hom.:

414

Bravo

AF:

0.129

Asia WGS

AF:

0.0790

AC:

278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.3

(source)

DANN

Benign

0.65

PhyloP100

0.20

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