dbSNP rs11679180: LINC01807:n.76-33014C>T (chr2-228777706-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 ENST00000665053.1(LINC01807):n.76-33014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,536 control chromosomes in the GnomAD database, including 2,922 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 0.19 ( 2922 hom., cov: 32)

Consequence

LINC01807
ENST00000665053.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.380

Publications

4 publications found

Variant links:

Genes affected

LINC01807 (HGNC:52610): (long intergenic non-protein coding RNA 1807)

LINC01807 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 = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01807	ENST00000665053.1 link	n.76-33014C>T	intron_variant	Intron 1 of 5
LINC01807	ENST00000667233.2 link	n.321-33014C>T	intron_variant	Intron 1 of 3
LINC01807	ENST00000787811.1 link	n.302-33018C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28414

AN:

151416

Hom.:

2920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.204

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

GnomAD4 genome

AF:

0.188

AC:

28427

AN:

151536

Hom.:

2922

Cov.:

AF XY:

0.182

AC XY:

13500

AN XY:

74038

show subpopulations

African (AFR)

AF:

0.107

AC:

4413

AN:

41138

American (AMR)

AF:

0.161

AC:

2459

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

548

AN:

3468

East Asian (EAS)

AF:

0.212

AC:

1085

AN:

5114

South Asian (SAS)

AF:

0.171

AC:

820

AN:

4792

European-Finnish (FIN)

AF:

0.163

AC:

1722

AN:

10560

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.246

AC:

16712

AN:

67906

Other (OTH)

AF:

0.203

AC:

426

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1169

2338

3507

4676

5845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.225

Hom.:

6858

Bravo

AF:

0.183

Asia WGS

AF:

0.171

AC:

595

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.22

(source)

DANN

Benign

0.36

PhyloP100

-0.38

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