Genetic Variant LINC01395:n.818T>C (chr11-129612280-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000631195.1(LINC01395):n.818T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,992 control chromosomes in the GnomAD database, including 37,458 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 0.70 ( 37455 hom., cov: 31)

Exomes 𝑓: 0.67 ( 3 hom. )

Consequence

LINC01395
ENST00000631195.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

LINC01395 (HGNC:50674): (long intergenic non-protein coding RNA 1395)

LINC01395 links:

ENSG00000281386 (HGNC:):

ENSG00000281386 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01395	NR_120582.1 link	n.818T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01395	ENST00000631195.1 link	n.818T>C		non_coding_transcript_exon_variant	Exon 4 of 4	1
ENSG00000281386	ENST00000626400.1 link	n.*170A>G		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106431

AN:

151862

Hom.:

37445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.599

Gnomad AMR

AF:

0.745

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.804

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.803

Gnomad NFE

AF:

0.719

Gnomad OTH

AF:

0.716

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.800

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.625

GnomAD4 genome

AF:

0.701

AC:

106483

AN:

151980

Hom.:

37455

Cov.:

AF XY:

0.702

AC XY:

52137

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.745

Gnomad4 ASJ

AF:

0.693

Gnomad4 EAS

AF:

0.778

Gnomad4 SAS

AF:

0.805

Gnomad4 FIN

AF:

0.663

Gnomad4 NFE

AF:

0.719

Gnomad4 OTH

AF:

0.715

Alfa

AF:

0.722

Hom.:

51914

Bravo

AF:

0.703

Asia WGS

AF:

0.788

AC:

2739

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.0

DANN

Benign

0.51

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