Genetic Variant LINC02900:n.1857T>A (chr5-135236539-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000505663.1(LINC02900):n.1857T>A 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 0.0394 in 151,944 control chromosomes in the GnomAD database, including 230 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 0.039 ( 230 hom., cov: 29)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

LINC02900
ENST00000505663.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0960

Publications

6 publications found

Variant links:

Genes affected

LINC02900 (HGNC:27964): (long intergenic non-protein coding RNA 2900)

LINC02900 links:

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

PITX1-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02900	NR_037895.1 link	n.1855T>A		non_coding_transcript_exon_variant	Exon 4 of 4
PITX1-AS1	NR_161235.1 link	n.467+62367A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02900	ENST00000505663.1 link	n.1857T>A	non_coding_transcript_exon_variant	Exon 4 of 4	1
PITX1-AS1	ENST00000513931.2 link	n.341-59956A>T	intron_variant	Intron 2 of 3	3
PITX1-AS1	ENST00000624272.3 link	n.461+62367A>T	intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.0392

AC:

5948

AN:

151588

Hom.:

225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0747

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.0786

Gnomad SAS

AF:

0.0244

Gnomad FIN

AF:

0.0399

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.00518

Gnomad OTH

AF:

0.0383

GnomAD4 exome

AF:

0.0126

AC:

AN:

238

Hom.:

Cov.:

AF XY:

0.00735

AC XY:

AN XY:

136

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0259

AC:

AN:

116

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0394

AC:

5980

AN:

151706

Hom.:

230

Cov.:

AF XY:

0.0418

AC XY:

3101

AN XY:

74108

show subpopulations

African (AFR)

AF:

0.0837

AC:

3454

AN:

41286

American (AMR)

AF:

0.0745

AC:

1138

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3470

East Asian (EAS)

AF:

0.0789

AC:

404

AN:

5118

South Asian (SAS)

AF:

0.0242

AC:

116

AN:

4796

European-Finnish (FIN)

AF:

0.0399

AC:

420

AN:

10514

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00518

AC:

352

AN:

67930

Other (OTH)

AF:

0.0379

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

283

567

850

1134

1417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.000530

Hom.:

22657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

(source)

DANN

Benign

0.54

PhyloP100

-0.096

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