dbSNP rs2898290: LINC00208:n.88T>C (chr8-11576400-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000304233.3(LINC00208):n.88T>C 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 0.481 in 153,118 control chromosomes in the GnomAD database, including 18,835 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 0.48 ( 18722 hom., cov: 31)

Exomes 𝑓: 0.42 ( 113 hom. )

Consequence

LINC00208
ENST00000304233.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870

Publications

46 publications found

Variant links:

Genes affected

LINC00208 (HGNC:15535): (long intergenic non-protein coding RNA 208)

LINC00208 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00208	NR_040035.1 link	n.-135T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00208	ENST00000304233.3 link	n.88T>C	non_coding_transcript_exon_variant	Exon 1 of 3	2
LINC00208	ENST00000652958.1 link	n.123T>C	non_coding_transcript_exon_variant	Exon 1 of 3
LINC00208	ENST00000653131.1 link	n.144T>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73180

AN:

151896

Hom.:

18717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.0203

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.485

GnomAD4 exome

AF:

0.424

AC:

468

AN:

1104

Hom.:

113

Cov.:

AF XY:

0.422

AC XY:

258

AN XY:

612

show subpopulations

African (AFR)

AF:

0.583

AC:

AN:

American (AMR)

AF:

0.400

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

0.0429

AC:

AN:

140

South Asian (SAS)

AF:

0.400

AC:

AN:

European-Finnish (FIN)

AF:

0.408

AC:

AN:

152

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.495

AC:

329

AN:

664

Other (OTH)

AF:

0.371

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.482

AC:

73215

AN:

152014

Hom.:

18722

Cov.:

AF XY:

0.467

AC XY:

34701

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.540

AC:

22401

AN:

41454

American (AMR)

AF:

0.386

AC:

5898

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

2147

AN:

3472

East Asian (EAS)

AF:

0.0201

AC:

104

AN:

5170

South Asian (SAS)

AF:

0.295

AC:

1420

AN:

4808

European-Finnish (FIN)

AF:

0.390

AC:

4128

AN:

10584

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.524

AC:

35626

AN:

67934

Other (OTH)

AF:

0.480

AC:

1010

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1864

3728

5593

7457

9321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<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:

0.511

Hom.:

59674

Bravo

AF:

0.480

Asia WGS

AF:

0.185

AC:

648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

DANN

Benign

0.25

PhyloP100

-0.87

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