Genetic Variant LINC02794:n.541-306G>A (chr1-48083641-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000635446.1(LINC02794):n.541-306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,142 control chromosomes in the GnomAD database, including 1,540 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 0.13 ( 1540 hom., cov: 32)

Consequence

LINC02794
ENST00000635446.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.495

Publications

3 publications found

Variant links:

Genes affected

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

LINC02794 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02794	XR_007066068.1 link	n.1429-306G>A	intron_variant	Intron 4 of 12
LINC02794	XR_007066069.1 link	n.1429-306G>A	intron_variant	Intron 4 of 10
LINC02794	XR_007066070.1 link	n.1429-306G>A	intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02794	ENST00000635446.1 link	n.541-306G>A		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19179

AN:

152024

Hom.:

1538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0316

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.126

AC:

19185

AN:

152142

Hom.:

1540

Cov.:

AF XY:

0.128

AC XY:

9502

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0315

AC:

1309

AN:

41534

American (AMR)

AF:

0.127

AC:

1948

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

541

AN:

3468

East Asian (EAS)

AF:

0.151

AC:

779

AN:

5158

South Asian (SAS)

AF:

0.175

AC:

841

AN:

4816

European-Finnish (FIN)

AF:

0.186

AC:

1965

AN:

10570

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11316

AN:

67994

Other (OTH)

AF:

0.117

AC:

247

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

846

1693

2539

3386

4232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.138

Hom.:

2620

Bravo

AF:

0.119

Asia WGS

AF:

0.160

AC:

556

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.0

(source)

DANN

Benign

0.43

PhyloP100

0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over