Genetic Variant LINC00598:n.142+374T>G (chr13-40535292-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000615137.1(LINC00598):n.142+374T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,216 control chromosomes in the GnomAD database, including 2,580 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 ( 2580 hom., cov: 33)

Consequence

LINC00598
ENST00000615137.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118

Publications

28 publications found

Variant links:

Genes affected

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

LINC00598 links:

ENSG00000288542 (HGNC:):

ENSG00000288542 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000615137.1 link	n.142+374T>G		intron_variant	Intron 1 of 3	3
ENSG00000288542	ENST00000636651.2 link	n.1459+24217T>G		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26753

AN:

152098

Hom.:

2577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.176

AC:

26777

AN:

152216

Hom.:

2580

Cov.:

AF XY:

0.172

AC XY:

12778

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.224

AC:

9282

AN:

41520

American (AMR)

AF:

0.171

AC:

2611

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

546

AN:

3472

East Asian (EAS)

AF:

0.320

AC:

1656

AN:

5170

South Asian (SAS)

AF:

0.113

AC:

547

AN:

4820

European-Finnish (FIN)

AF:

0.102

AC:

1077

AN:

10608

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10273

AN:

68016

Other (OTH)

AF:

0.223

AC:

470

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1158

2315

3473

4630

5788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.166

Hom.:

9614

Bravo

AF:

0.185

Asia WGS

AF:

0.213

AC:

741

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

0.12

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