Genetic Variant ENST00000506090.6:n.468+94G>T (chr15-88603303-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 ENST00000506090.6(LINC01586):n.468+94G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,882 control chromosomes in the GnomAD database, including 14,725 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 0.44 ( 14725 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

LINC01586
ENST00000506090.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.569

Publications

7 publications found

Variant links:

Genes affected

LINC01586 (HGNC:51434): (long intergenic non-protein coding RNA 1586)

LINC01586 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01586	NR_120369.1 link	n.343+94G>T		intron_variant	Intron 2 of 2
LINC01586	NR_120370.1 link	n.333+94G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01586	ENST00000506090.6 link	n.468+94G>T	intron_variant	Intron 2 of 2	2
LINC01586	ENST00000560368.1 link	n.333+94G>T	intron_variant	Intron 2 of 2	3
LINC01586	ENST00000660022.1 link	n.119+94G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66631

AN:

151764

Hom.:

14724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.718

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.450

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

GnomAD4 genome

AF:

0.439

AC:

66662

AN:

151882

Hom.:

14725

Cov.:

AF XY:

0.440

AC XY:

32659

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.456

AC:

18875

AN:

41388

American (AMR)

AF:

0.422

AC:

6432

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

1343

AN:

3468

East Asian (EAS)

AF:

0.718

AC:

3719

AN:

5182

South Asian (SAS)

AF:

0.409

AC:

1971

AN:

4822

European-Finnish (FIN)

AF:

0.452

AC:

4752

AN:

10512

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.411

AC:

27961

AN:

67958

Other (OTH)

AF:

0.449

AC:

945

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1992

3984

5976

7968

9960

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.353

Hom.:

1466

Bravo

AF:

0.441

Asia WGS

AF:

0.569

AC:

1976

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.1

(source)

DANN

Benign

0.42

PhyloP100

0.57

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