dbSNP rs11121129: 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

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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