Genetic Variant LINC03069:n.1067+5672G>A (chr18-56050233-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000382897.2(LINC03069):n.1067+5672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,136 control chromosomes in the GnomAD database, including 943 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 0.10 ( 943 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LINC03069
ENST00000382897.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702

Variant links:

Genes affected

LINC03069 (HGNC:):

LINC03069 links:

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC01905 links:

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

LINC03069 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.23).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01905	NR_146510.1 link	n.165+56C>T	intron_variant	Intron 2 of 3
LINC01905	NR_146511.1 link	n.165+56C>T	intron_variant	Intron 2 of 2
LINC03069	NR_148972.1 link	n.1067+5672G>A	intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC03069	ENST00000382897.2 link	n.1067+5672G>A	intron_variant	Intron 6 of 8	2
LINC01905	ENST00000585684.5 link	n.210+7889C>T	intron_variant	Intron 1 of 1	2
LINC01905	ENST00000589450.5 link	n.49+56C>T	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15709

AN:

152016

Hom.:

941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0513

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.0968

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.0847

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.119

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.103

AC:

15706

AN:

152136

Hom.:

943

Cov.:

AF XY:

0.103

AC XY:

7690

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.0512

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.0968

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.0847

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.126

Hom.:

1639

Bravo

AF:

0.103

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.71

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