Genetic Variant ENST00000706980.1:n.464+11643G>T (chr13-54041638-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000706980.1(LINC00458):n.464+11643G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,078 control chromosomes in the GnomAD database, including 2,663 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 ( 2663 hom., cov: 32)

Consequence

LINC00458
ENST00000706980.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00400

Publications

14 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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
LINC00458	ENST00000706980.1 link	n.464+11643G>T		intron_variant	Intron 4 of 10
LINC00458	ENST00000706981.1 link	n.570+54468G>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27738

AN:

151958

Hom.:

2653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.179

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

GnomAD4 genome

AF:

0.183

AC:

27782

AN:

152078

Hom.:

2663

Cov.:

AF XY:

0.185

AC XY:

13716

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.193

AC:

8007

AN:

41494

American (AMR)

AF:

0.261

AC:

3983

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

486

AN:

3468

East Asian (EAS)

AF:

0.137

AC:

708

AN:

5168

South Asian (SAS)

AF:

0.204

AC:

985

AN:

4820

European-Finnish (FIN)

AF:

0.173

AC:

1829

AN:

10578

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11256

AN:

67988

Other (OTH)

AF:

0.180

AC:

379

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1142

2283

3425

4566

5708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.159

Hom.:

2903

Bravo

AF:

0.187

Asia WGS

AF:

0.197

AC:

689

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

0.78

(source)

DANN

Benign

0.56

PhyloP100

0.0040

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