Genetic Variant LINC01208:n.349+6433C>T (chr3-176484906-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 ENST00000652470.1(LINC01208):n.349+6433C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,140 control chromosomes in the GnomAD database, including 2,036 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 0.15 ( 2036 hom., cov: 32)

Consequence

LINC01208
ENST00000652470.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.244

Publications

0 publications found

Variant links:

Genes affected

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

LINC01208 links:

ENSG00000302303 (HGNC:):

ENSG00000302303 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01208	ENST00000652470.1 link	n.349+6433C>T	intron_variant	Intron 3 of 5
ENSG00000302303	ENST00000785650.1 link	n.74+7436G>A	intron_variant	Intron 1 of 2
LINC01208	ENST00000785771.1 link	n.69+6433C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22865

AN:

152024

Hom.:

2034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0835

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.00117

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.152

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

GnomAD4 genome

AF:

0.150

AC:

22878

AN:

152140

Hom.:

2036

Cov.:

AF XY:

0.145

AC XY:

10775

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0836

AC:

3471

AN:

41524

American (AMR)

AF:

0.132

AC:

2022

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

509

AN:

3472

East Asian (EAS)

AF:

0.00117

AC:

AN:

5136

South Asian (SAS)

AF:

0.104

AC:

502

AN:

4824

European-Finnish (FIN)

AF:

0.160

AC:

1691

AN:

10590

Middle Eastern (MID)

AF:

0.113

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.208

AC:

14135

AN:

67992

Other (OTH)

AF:

0.150

AC:

317

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

987

1974

2960

3947

4934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.104

Hom.:

186

Bravo

AF:

0.147

Asia WGS

AF:

0.0480

AC:

165

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.0

(source)

DANN

Benign

0.15

PhyloP100

0.24

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