Genetic Variant LINC02141:n.174-12886A>G (chr16-60031825-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000568279.2(LINC02141):n.174-12886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 152,074 control chromosomes in the GnomAD database, including 1,144 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 0.10 ( 1144 hom., cov: 32)

Consequence

LINC02141
ENST00000568279.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109

Publications

2 publications found

Variant links:

Genes affected

LINC02141 (HGNC:53001): (long intergenic non-protein coding RNA 2141)

LINC02141 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02141	NR_110917.1 link	n.174-12886A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02141	ENST00000568279.2 link	n.174-12886A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.0996

AC:

15138

AN:

151956

Hom.:

1135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.0814

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.0328

Gnomad MID

AF:

0.0637

Gnomad NFE

AF:

0.0436

Gnomad OTH

AF:

0.0926

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

GnomAD4 genome

AF:

0.0999

AC:

15188

AN:

152074

Hom.:

1144

Cov.:

AF XY:

0.101

AC XY:

7497

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.195

AC:

8069

AN:

41460

American (AMR)

AF:

0.119

AC:

1814

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0814

AC:

282

AN:

3466

East Asian (EAS)

AF:

0.174

AC:

897

AN:

5142

South Asian (SAS)

AF:

0.121

AC:

586

AN:

4828

European-Finnish (FIN)

AF:

0.0328

AC:

348

AN:

10596

Middle Eastern (MID)

AF:

0.0616

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0436

AC:

2965

AN:

68002

Other (OTH)

AF:

0.0917

AC:

194

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

657

1314

1970

2627

3284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0733

Hom.:

Bravo

AF:

0.110

Asia WGS

AF:

0.139

AC:

482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.0

(source)

DANN

Benign

0.47

PhyloP100

0.11

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