Variant rs4905757 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_161367.1(LINC02914):n.649T>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 0.0458 in 1,614,048 control chromosomes in the GnomAD database, including 2,258 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 0.038 ( 177 hom., cov: 32)

Exomes 𝑓: 0.047 ( 2081 hom. )

Consequence

LINC02914
NR_161367.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660

Variant links:

Genes affected

LINC02914 (HGNC:26375): (long intergenic non-protein coding RNA 2914)

LINC02914 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 (MetaRNN=0.0022147).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LINC02914	NR_161367.1 linkuse as main transcript	n.649T>C	non_coding_transcript_exon_variant	4/5
LINC02914	NR_161368.1 linkuse as main transcript	n.517T>C	non_coding_transcript_exon_variant	3/4
LINC02914	NR_161369.1 linkuse as main transcript	n.347T>C	non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02914	ENST00000650364.1 linkuse as main transcript	n.517T>C		non_coding_transcript_exon_variant	3/4
LINC02914	ENST00000541516.1 linkuse as main transcript	n.340T>C		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5720

AN:

152142

Hom.:

177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00960

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.0630

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0524

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0388

AC:

9741

AN:

250956

Hom.:

286

AF XY:

0.0393

AC XY:

5330

AN XY:

135644

show subpopulations

Gnomad AFR exome

AF:

0.00752

Gnomad AMR exome

AF:

0.0251

Gnomad ASJ exome

AF:

0.0906

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0142

Gnomad FIN exome

AF:

0.0565

Gnomad NFE exome

AF:

0.0520

Gnomad OTH exome

AF:

0.0464

GnomAD4 exome

AF:

0.0467

AC:

68195

AN:

1461788

Hom.:

2081

Cov.:

AF XY:

0.0458

AC XY:

33335

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.00818

Gnomad4 AMR exome

AF:

0.0265

Gnomad4 ASJ exome

AF:

0.0896

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0142

Gnomad4 FIN exome

AF:

0.0534

Gnomad4 NFE exome

AF:

0.0514

Gnomad4 OTH exome

AF:

0.0458

GnomAD4 genome

AF:

0.0376

AC:

5723

AN:

152260

Hom.:

177

Cov.:

AF XY:

0.0375

AC XY:

2796

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00958

Gnomad4 AMR

AF:

0.0340

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0131

Gnomad4 FIN

AF:

0.0630

Gnomad4 NFE

AF:

0.0524

Gnomad4 OTH

AF:

0.0417

Alfa

AF:

0.0512

Hom.:

576

Bravo

AF:

0.0349

TwinsUK

AF:

0.0574

AC:

213

ALSPAC

AF:

0.0509

AC:

196

ESP6500AA

AF:

0.00749

AC:

ESP6500EA

AF:

0.0538

AC:

463

ExAC

AF:

0.0372

AC:

4522

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.0547

EpiControl

AF:

0.0542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.66

CADD

Benign

1.1

DANN

Benign

0.47

DEOGEN2

Benign

0.053

Eigen

Benign

-0.90

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0022

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

PROVEAN

Uncertain

-4.0

REVEL

Benign

0.058

Polyphen

0.50

Vest4

0.077

MPC

0.0099

ClinPred

0.055

GERP RS

-0.47

Varity_R

0.43

gMVP

0.0021

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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