Genetic Variant ENST00000652470.1:n.350-741A>G (chr3-176421737-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 ENST00000652470.1(LINC01208):n.350-741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,182 control chromosomes in the GnomAD database, including 1,203 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 0.12 ( 1203 hom., cov: 32)

Consequence

LINC01208
ENST00000652470.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222

Publications

3 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 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.350-741A>G	intron_variant	Intron 3 of 5
LINC01208	ENST00000785771.1 link	n.70-741A>G	intron_variant	Intron 1 of 2
LINC01208	ENST00000785773.1 link	n.122-741A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17589

AN:

152064

Hom.:

1200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0699

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.0984

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.000961

Gnomad SAS

AF:

0.0577

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.0577

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.116

AC:

17603

AN:

152182

Hom.:

1203

Cov.:

AF XY:

0.110

AC XY:

8217

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0698

AC:

2900

AN:

41564

American (AMR)

AF:

0.0983

AC:

1502

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

396

AN:

3470

East Asian (EAS)

AF:

0.000963

AC:

AN:

5190

South Asian (SAS)

AF:

0.0578

AC:

279

AN:

4830

European-Finnish (FIN)

AF:

0.128

AC:

1355

AN:

10596

Middle Eastern (MID)

AF:

0.0586

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.159

AC:

10813

AN:

67946

Other (OTH)

AF:

0.126

AC:

266

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

782

1564

2347

3129

3911

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.144

Hom.:

835

Bravo

AF:

0.114

Asia WGS

AF:

0.0370

AC:

129

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.70

PhyloP100

-0.22

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