Variant chr13-54180396-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000706980.1(LINC00458):n.120-52967A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,208 control chromosomes in the GnomAD database, including 70,906 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 ( 70906 hom., cov: 31)

Consequence

LINC00458
ENST00000706980.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Variant links:

Genes affected

LINC00458 (HGNC:42807): (long intergenic non-protein coding RNA 458)

LINC00458 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
LINC00458	ENST00000706980.1 link	n.120-52967A>G	intron_variant
LINC00458	ENST00000706981.1 link	n.200-52967A>G	intron_variant
LINC00458	ENST00000706986.1 link	n.110+2988A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.965

AC:

146771

AN:

152090

Hom.:

70857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.952

Gnomad AMI

AF:

0.988

Gnomad AMR

AF:

0.972

Gnomad ASJ

AF:

0.974

Gnomad EAS

AF:

0.893

Gnomad SAS

AF:

0.991

Gnomad FIN

AF:

0.975

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.967

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

GnomAD4 genome

AF:

0.965

AC:

146878

AN:

152208

Hom.:

70906

Cov.:

AF XY:

0.965

AC XY:

71819

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.952

Gnomad4 AMR

AF:

0.973

Gnomad4 ASJ

AF:

0.974

Gnomad4 EAS

AF:

0.893

Gnomad4 SAS

AF:

0.991

Gnomad4 FIN

AF:

0.975

Gnomad4 NFE

AF:

0.972

Gnomad4 OTH

AF:

0.965

Alfa

AF:

0.971

Hom.:

8341

Bravo

AF:

0.963

Asia WGS

AF:

0.954

AC:

3315

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

0.97

DANN

Benign

0.76

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