Genetic Variant LINC01682:n.401-848T>G (chr1-229876569-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The ENST00000435973.3(LINC01682):n.401-848T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,182 control chromosomes in the GnomAD database, including 10,181 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 0.20 ( 10181 hom., cov: 32)

Consequence

LINC01682
ENST00000435973.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

Publications

4 publications found

Variant links:

Genes affected

LINC01682 (HGNC:52470): (long intergenic non-protein coding RNA 1682)

LINC01682 links:

ENSG00000304899 (HGNC:):

ENSG00000304899 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01682	NR_146476.1 link	n.280-848T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01682	ENST00000435973.3 link	n.401-848T>G	intron_variant	Intron 2 of 2	2
LINC01682	ENST00000650825.1 link	n.44-848T>G	intron_variant	Intron 1 of 8
LINC01682	ENST00000661713.1 link	n.336-848T>G	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30574

AN:

152064

Hom.:

10155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.692

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0816

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.00448

Gnomad OTH

AF:

0.149

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

GnomAD4 genome

AF:

0.201

AC:

30646

AN:

152182

Hom.:

10181

Cov.:

AF XY:

0.194

AC XY:

14448

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.692

AC:

28680

AN:

41448

American (AMR)

AF:

0.0814

AC:

1245

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0110

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5182

South Asian (SAS)

AF:

0.00767

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000188

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00447

AC:

304

AN:

68018

Other (OTH)

AF:

0.148

AC:

313

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

519

1038

1556

2075

2594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.135

Hom.:

2553

Bravo

AF:

0.231

Asia WGS

AF:

0.0520

AC:

183

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

(source)

DANN

Benign

0.82

PhyloP100

-0.65

Mutation Taster

=100/0

polymorphism

(source)

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