Genetic Variant LINC00598:n.70+20442A>G (chr13-40439840-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 ENST00000636621.1(LINC00598):n.70+20442A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,288 control chromosomes in the GnomAD database, including 45,975 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 0.78 ( 45860 hom., cov: 29)

Exomes 𝑓: 0.77 ( 115 hom. )

Consequence

LINC00598
ENST00000636621.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

52 publications found

Variant links:

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

LINC00598 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00598	NR_024506.2 link	n.661+20442A>G		intron_variant	Intron 5 of 5
LINC00598	NR_024507.3 link	n.801+11224A>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00598	ENST00000636621.1 link	n.70+20442A>G	intron_variant	Intron 1 of 1	1
LINC00598	ENST00000782816.1 link	n.195A>G	non_coding_transcript_exon_variant	Exon 1 of 3
LINC00598	ENST00000637523.1 link	n.658+11224A>G	intron_variant	Intron 5 of 10	5

Frequencies

GnomAD3 genomes

AF:

0.776

AC:

117802

AN:

151780

Hom.:

45818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.802

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.841

Gnomad SAS

AF:

0.940

Gnomad FIN

AF:

0.732

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.752

Gnomad OTH

AF:

0.779

GnomAD4 exome

AF:

0.769

AC:

300

AN:

390

Hom.:

115

AF XY:

0.766

AC XY:

164

AN XY:

214

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.833

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.800

AC:

AN:

East Asian (EAS)

AF:

0.841

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.853

AC:

AN:

Middle Eastern (MID)

AF:

0.833

AC:

AN:

European-Non Finnish (NFE)

AF:

0.725

AC:

187

AN:

258

Other (OTH)

AF:

0.950

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.776

AC:

117898

AN:

151898

Hom.:

45860

Cov.:

AF XY:

0.777

AC XY:

57665

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.785

AC:

32529

AN:

41416

American (AMR)

AF:

0.803

AC:

12258

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.822

AC:

2850

AN:

3468

East Asian (EAS)

AF:

0.841

AC:

4335

AN:

5152

South Asian (SAS)

AF:

0.938

AC:

4510

AN:

4806

European-Finnish (FIN)

AF:

0.732

AC:

7705

AN:

10520

Middle Eastern (MID)

AF:

0.827

AC:

243

AN:

294

European-Non Finnish (NFE)

AF:

0.752

AC:

51072

AN:

67954

Other (OTH)

AF:

0.780

AC:

1645

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1333

2665

3998

5330

6663

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<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:

0.764

Hom.:

205700

Bravo

AF:

0.779

Asia WGS

AF:

0.891

AC:

3098

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.6

(source)

DANN

Benign

0.83

PhyloP100

0.11

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

Other links and lift over