Genetic Variant ENST00000428516.1:n.198+84029T>A (chr3-176769680-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000428516.1(LINC01208):n.198+84029T>A 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 0.15 ( 446 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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

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>A		intron_variant	Intron 2 of 4	5
LINC01208	ENST00000794389.1 link	n.187-47695T>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

3913

AN:

25880

Hom.:

445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.0656

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.273

Gnomad NFE

AF:

0.0930

Gnomad OTH

AF:

0.160

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

GnomAD4 genome

AF:

0.151

AC:

3924

AN:

25910

Hom.:

446

Cov.:

AF XY:

0.159

AC XY:

1898

AN XY:

11904

show subpopulations

African (AFR)

AF:

0.267

AC:

1742

AN:

6534

American (AMR)

AF:

0.176

AC:

392

AN:

2224

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

AN:

768

East Asian (EAS)

AF:

0.233

AC:

197

AN:

844

South Asian (SAS)

AF:

0.119

AC:

AN:

480

European-Finnish (FIN)

AF:

0.122

AC:

109

AN:

896

Middle Eastern (MID)

AF:

0.273

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0931

AC:

1264

AN:

13584

Other (OTH)

AF:

0.159

AC:

AN:

314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

164

247

329

411

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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

-0.90

CADD

Benign

2.7

(source)

DANN

Benign

0.32

PhyloP100

0.061

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