dbSNP rs560004: LINC02794:n.595T>C (chr1-48084001-T-C) – 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.595T>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 0.355 in 152,106 control chromosomes in the GnomAD database, including 10,455 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 0.35 ( 10455 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

LINC02794
ENST00000635446.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.545

Publications

3 publications found

Variant links:

COSMIC-nc: COSV71692447

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02794	XR_007066068.1 link	n.1483T>C	non_coding_transcript_exon_variant	Exon 5 of 13
LINC02794	XR_007066069.1 link	n.1483T>C	non_coding_transcript_exon_variant	Exon 5 of 11
LINC02794	XR_007066070.1 link	n.1483T>C	non_coding_transcript_exon_variant	Exon 5 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02794	ENST00000635446.1 link	n.595T>C		non_coding_transcript_exon_variant	Exon 5 of 6	3

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53924

AN:

151986

Hom.:

10446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.379

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.386

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.355

AC:

53935

AN:

152104

Hom.:

10455

Cov.:

AF XY:

0.361

AC XY:

26814

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.209

AC:

8688

AN:

41508

American (AMR)

AF:

0.499

AC:

7623

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1094

AN:

3470

East Asian (EAS)

AF:

0.623

AC:

3219

AN:

5164

South Asian (SAS)

AF:

0.392

AC:

1890

AN:

4822

European-Finnish (FIN)

AF:

0.379

AC:

3999

AN:

10556

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.385

AC:

26156

AN:

67988

Other (OTH)

AF:

0.390

AC:

823

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1719

3438

5157

6876

8595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.382

Hom.:

38918

Bravo

AF:

0.358

Asia WGS

AF:

0.502

AC:

1744

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.1

(source)

DANN

Benign

0.70

PhyloP100

0.55

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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