Variant chr13-40374014-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_024506.1(LINC00598):n.664-23712G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,322 control chromosomes in the GnomAD database, including 70,875 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 0.96 ( 70875 hom., cov: 32)

Consequence

LINC00598
NR_024506.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.68

Variant links:

Genes affected

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

LINC00598 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00598	NR_024506.1 linkuse as main transcript	n.664-23712G>A		intron_variant, non_coding_transcript_variant
LINC00598	NR_024507.2 linkuse as main transcript	n.804-23712G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC00598	ENST00000636621.1 linkuse as main transcript	n.71-23712G>A	intron_variant, non_coding_transcript_variant	1
LINC00598	ENST00000400432.4 linkuse as main transcript	n.117-23712G>A	intron_variant, non_coding_transcript_variant	5
LINC00598	ENST00000636192.2 linkuse as main transcript	n.178-23712G>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.965

AC:

146807

AN:

152204

Hom.:

70821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.945

Gnomad AMI

AF:

0.953

Gnomad AMR

AF:

0.976

Gnomad ASJ

AF:

0.970

Gnomad EAS

AF:

0.988

Gnomad SAS

AF:

0.937

Gnomad FIN

AF:

0.938

Gnomad MID

AF:

0.930

Gnomad NFE

AF:

0.979

Gnomad OTH

AF:

0.961

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

GnomAD4 genome

AF:

0.965

AC:

146920

AN:

152322

Hom.:

70875

Cov.:

AF XY:

0.963

AC XY:

71702

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.945

Gnomad4 AMR

AF:

0.976

Gnomad4 ASJ

AF:

0.970

Gnomad4 EAS

AF:

0.988

Gnomad4 SAS

AF:

0.936

Gnomad4 FIN

AF:

0.938

Gnomad4 NFE

AF:

0.979

Gnomad4 OTH

AF:

0.961

Alfa

AF:

0.969

Hom.:

10017

Bravo

AF:

0.967

Asia WGS

AF:

0.956

AC:

3327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.016

DANN

Benign

0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over