Genetic Variant LINC01579:n.195+3712C>A (chr15-93825268-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000553818.1(LINC01579):n.195+3712C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0000081 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LINC01579
ENST00000553818.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

Publications

1 publications found

Variant links:

Genes affected

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

LINC01579 links:

ENSG00000258627 (HGNC:):

ENSG00000258627 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01579	ENST00000553818.1 link	n.195+3712C>A	intron_variant	Intron 1 of 3	4
LINC01579	ENST00000557481.6 link	n.431-4168C>A	intron_variant	Intron 3 of 6	5
LINC01579	ENST00000766606.1 link	n.724-4168C>A	intron_variant	Intron 3 of 4
ENSG00000258627	ENST00000555468.1 link	n.-109C>A	upstream_gene_variant		6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000814

AC:

AN:

245748

Hom.:

AF XY:

0.0000141

AC XY:

AN XY:

142120

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

5384

American (AMR)

AF:

0.00

AC:

AN:

15050

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5742

East Asian (EAS)

AF:

0.00

AC:

AN:

9086

South Asian (SAS)

AF:

0.0000242

AC:

AN:

41330

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17324

Middle Eastern (MID)

AF:

0.00

AC:

AN:

934

European-Non Finnish (NFE)

AF:

0.00000717

AC:

AN:

139494

Other (OTH)

AF:

0.00

AC:

AN:

11404

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.60

(source)

DANN

Benign

0.37

PhyloP100

-2.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over