Variant rs1951082 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_110033.1(LINC02294):n.306-15138A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,732 control chromosomes in the GnomAD database, including 21,119 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 0.49 ( 21119 hom., cov: 29)

Consequence

LINC02294
NR_110033.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Variant links:

Genes affected

LINC02294 (HGNC:53210): (long intergenic non-protein coding RNA 2294)

LINC02294 links:

(HGNC:):

links:

NOVA1-DT (HGNC:19827): (NOVA1 divergent transcript)

NOVA1-DT 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02294	NR_110033.1 linkuse as main transcript	n.306-15138A>T		intron_variant, non_coding_transcript_variant
NOVA1-DT	NR_147061.1 linkuse as main transcript	n.2020+8629T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02294	ENST00000549330.1 linkuse as main transcript	n.293-15138A>T	intron_variant, non_coding_transcript_variant	2
	ENST00000656336.1 linkuse as main transcript	n.480+66043T>A	intron_variant, non_coding_transcript_variant
NOVA1-DT	ENST00000662478.1 linkuse as main transcript	n.1778-15399T>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74648

AN:

151614

Hom.:

21117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.638

Gnomad ASJ

AF:

0.476

Gnomad EAS

AF:

0.819

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.433

Gnomad NFE

AF:

0.589

Gnomad OTH

AF:

0.531

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

GnomAD4 genome

AF:

0.492

AC:

74647

AN:

151732

Hom.:

21119

Cov.:

AF XY:

0.499

AC XY:

36938

AN XY:

74092

show subpopulations

Gnomad4 AFR

AF:

0.203

Gnomad4 AMR

AF:

0.639

Gnomad4 ASJ

AF:

0.476

Gnomad4 EAS

AF:

0.818

Gnomad4 SAS

AF:

0.524

Gnomad4 FIN

AF:

0.609

Gnomad4 NFE

AF:

0.589

Gnomad4 OTH

AF:

0.528

Alfa

AF:

0.556

Hom.:

12322

Bravo

AF:

0.483

Asia WGS

AF:

0.609

AC:

2116

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.1

DANN

Benign

0.80

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