Genetic Variant LINC01714:n.106-632G>A (chr1-8208035-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000452982.2(LINC01714):n.106-632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,034 control chromosomes in the GnomAD database, including 5,403 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 0.26 ( 5403 hom., cov: 32)

Consequence

LINC01714
ENST00000452982.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.639

Publications

31 publications found

Variant links:

Genes affected

LINC01714 (HGNC:52501): (long intergenic non-protein coding RNA 1714)

LINC01714 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01714	ENST00000452982.2 link	n.106-632G>A	intron_variant	Intron 1 of 4	3
LINC01714	ENST00000635451.2 link	n.543-632G>A	intron_variant	Intron 1 of 3	5
LINC01714	ENST00000670361.1 link	n.239-632G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39406

AN:

151916

Hom.:

5400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.259

AC:

39411

AN:

152034

Hom.:

5403

Cov.:

AF XY:

0.258

AC XY:

19169

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.173

AC:

7188

AN:

41468

American (AMR)

AF:

0.373

AC:

5695

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

761

AN:

3466

East Asian (EAS)

AF:

0.286

AC:

1476

AN:

5160

South Asian (SAS)

AF:

0.292

AC:

1406

AN:

4816

European-Finnish (FIN)

AF:

0.235

AC:

2488

AN:

10568

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19592

AN:

67980

Other (OTH)

AF:

0.254

AC:

536

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1461

2923

4384

5846

7307

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.280

Hom.:

11088

Bravo

AF:

0.268

Asia WGS

AF:

0.301

AC:

1048

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.5

(source)

DANN

Benign

0.38

PhyloP100

0.64

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