Genetic Variant LINC01714:n.292C>T (chr1-8208853-C-T) – 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.292C>T 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 0.259 in 152,048 control chromosomes in the GnomAD database, including 5,396 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 ( 5395 hom., cov: 32)

Exomes 𝑓: 0.25 ( 1 hom. )

Consequence

LINC01714
ENST00000452982.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.422

Publications

5 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=-0.88).

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
LINC01714	NR_125998.1 link	n.182C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01714	ENST00000452982.2 link	n.292C>T	non_coding_transcript_exon_variant	Exon 2 of 5	3
LINC01714	ENST00000635451.2 link	n.729C>T	non_coding_transcript_exon_variant	Exon 2 of 4	5
LINC01714	ENST00000670361.1 link	n.425C>T	non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39373

AN:

151906

Hom.:

5392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.254

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.143

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.259

AC:

39379

AN:

152024

Hom.:

5395

Cov.:

AF XY:

0.258

AC XY:

19135

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.173

AC:

7190

AN:

41472

American (AMR)

AF:

0.373

AC:

5700

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

777

AN:

3472

East Asian (EAS)

AF:

0.279

AC:

1438

AN:

5162

South Asian (SAS)

AF:

0.292

AC:

1403

AN:

4808

European-Finnish (FIN)

AF:

0.235

AC:

2482

AN:

10564

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19583

AN:

67958

Other (OTH)

AF:

0.255

AC:

538

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1479

2958

4437

5916

7395

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:

0.160

Hom.:

309

Bravo

AF:

0.268

Asia WGS

AF:

0.299

AC:

1043

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.19

(source)

DANN

Benign

0.48

PhyloP100

-0.42

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over