dbSNP rs11683197: LINC01800:n.441+13158A>G (chr2-64800490-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 ENST00000772000.1(LINC01800):n.441+13158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,182 control chromosomes in the GnomAD database, including 4,303 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 0.22 ( 4303 hom., cov: 32)

Consequence

LINC01800
ENST00000772000.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Publications

5 publications found

Variant links:

Genes affected

LINC01800 (HGNC:52590): (long intergenic non-protein coding RNA 1800)

LINC01800 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 (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01800	ENST00000772000.1 link	n.441+13158A>G	intron_variant	Intron 2 of 3
LINC01800	ENST00000772002.1 link	n.322+13158A>G	intron_variant	Intron 2 of 3
LINC01800	ENST00000772003.1 link	n.210+13207A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34157

AN:

152064

Hom.:

4301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0990

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.319

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.241

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

GnomAD4 genome

AF:

0.225

AC:

34172

AN:

152182

Hom.:

4303

Cov.:

AF XY:

0.228

AC XY:

16949

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.0990

AC:

4114

AN:

41540

American (AMR)

AF:

0.238

AC:

3634

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.319

AC:

1106

AN:

3466

East Asian (EAS)

AF:

0.184

AC:

951

AN:

5176

South Asian (SAS)

AF:

0.407

AC:

1963

AN:

4822

European-Finnish (FIN)

AF:

0.278

AC:

2945

AN:

10582

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18621

AN:

67982

Other (OTH)

AF:

0.240

AC:

506

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1361

2722

4083

5444

6805

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.260

Hom.:

22851

Bravo

AF:

0.215

Asia WGS

AF:

0.270

AC:

938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.58

(source)

DANN

Benign

0.40

PhyloP100

-0.49

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