dbSNP rs2074193: LINC02156:n.9T>G (chr12-47377646-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000659658.1(LINC02156):n.9T>G 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 0.208 in 152,148 control chromosomes in the GnomAD database, including 3,505 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 0.21 ( 3505 hom., cov: 32)

Consequence

LINC02156
ENST00000659658.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.295

Variant links:

Genes affected

LINC02156 (HGNC:53017): (long intergenic non-protein coding RNA 2156)

LINC02156 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02156	ENST00000659658.1 link	n.9T>G	non_coding_transcript_exon_variant	Exon 1 of 3
LINC02156	ENST00000648410.1 link	n.-37T>G	upstream_gene_variant
LINC02156	ENST00000650246.1 link	n.-42T>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31566

AN:

152032

Hom.:

3506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.0473

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.243

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

GnomAD4 genome

AF:

0.208

AC:

31574

AN:

152148

Hom.:

3505

Cov.:

AF XY:

0.207

AC XY:

15432

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.222

Gnomad4 EAS

AF:

0.0474

Gnomad4 SAS

AF:

0.239

Gnomad4 FIN

AF:

0.225

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.244

Alfa

AF:

0.240

Hom.:

4383

Bravo

AF:

0.207

Asia WGS

AF:

0.172

AC:

599

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.0

DANN

Benign

0.68

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