Genetic Variant LINC01900:n.347+14497T>A (chr18-22058349-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000716236.1(LINC01900):n.347+14497T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,084 control chromosomes in the GnomAD database, including 2,694 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 0.17 ( 2694 hom., cov: 31)

Consequence

LINC01900
ENST00000716236.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

1 publications found

Variant links:

Genes affected

LINC01900 (HGNC:52719): (long intergenic non-protein coding RNA 1900)

LINC01900 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01900	ENST00000716236.1 link	n.347+14497T>A		intron_variant	Intron 3 of 4
LINC01900	ENST00000780669.1 link	n.348+14497T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25591

AN:

151966

Hom.:

2689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.168

AC:

25607

AN:

152084

Hom.:

2694

Cov.:

AF XY:

0.172

AC XY:

12810

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.238

AC:

9887

AN:

41476

American (AMR)

AF:

0.292

AC:

4461

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

353

AN:

3470

East Asian (EAS)

AF:

0.250

AC:

1291

AN:

5158

South Asian (SAS)

AF:

0.203

AC:

979

AN:

4818

European-Finnish (FIN)

AF:

0.112

AC:

1190

AN:

10584

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6919

AN:

67998

Other (OTH)

AF:

0.167

AC:

353

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1008

2016

3024

4032

5040

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.142

Hom.:

217

Bravo

AF:

0.185

Asia WGS

AF:

0.239

AC:

829

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.8

(source)

DANN

Benign

0.75

PhyloP100

-1.1

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