dbSNP rs9882505: LINC01208:n.198+84029T>C (chr3-176769680-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000428516.1(LINC01208):n.198+84029T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00038 ( 0 hom., cov: 0)

Consequence

LINC01208
ENST00000428516.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610

Publications

1 publications found

Variant links:

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

LINC01208 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01208	ENST00000428516.1 link	n.198+84029T>C		intron_variant	Intron 2 of 4	5
LINC01208	ENST00000794389.1 link	n.187-47695T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.000383

AC:

AN:

26096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000457

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000447

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00117

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00223

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000146

Gnomad OTH

AF:

0.00316

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

GnomAD4 genome

AF:

0.000383

AC:

AN:

26126

Hom.:

Cov.:

AF XY:

0.000500

AC XY:

AN XY:

12004

show subpopulations

African (AFR)

AF:

0.000455

AC:

AN:

6596

American (AMR)

AF:

0.000447

AC:

AN:

2238

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

772

East Asian (EAS)

AF:

0.00117

AC:

AN:

856

South Asian (SAS)

AF:

0.00

AC:

AN:

486

European-Finnish (FIN)

AF:

0.00223

AC:

AN:

898

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000146

AC:

AN:

13690

Other (OTH)

AF:

0.00314

AC:

AN:

318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

(source)

DANN

Benign

0.27

PhyloP100

0.061

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