dbSNP rs10498230: LINC01807:n.125+106856G>A (chr2-228637787-C-T) – 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.125+106856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,158 control chromosomes in the GnomAD database, including 437 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 0.074 ( 437 hom., cov: 32)

Consequence

LINC01807
ENST00000665053.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.185

Publications

16 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=-1.03).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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
LINC01807	ENST00000665053.1 link	n.125+106856G>A		intron_variant	Intron 2 of 5
LINC01807	ENST00000667233.2 link	n.370+106856G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

11238

AN:

152040

Hom.:

428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0676

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0862

Gnomad ASJ

AF:

0.0505

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0412

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0723

Gnomad OTH

AF:

0.0662

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

GnomAD4 genome

AF:

0.0741

AC:

11268

AN:

152158

Hom.:

437

Cov.:

AF XY:

0.0748

AC XY:

5564

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0677

AC:

2812

AN:

41512

American (AMR)

AF:

0.0865

AC:

1322

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0505

AC:

175

AN:

3468

East Asian (EAS)

AF:

0.139

AC:

717

AN:

5160

South Asian (SAS)

AF:

0.146

AC:

703

AN:

4820

European-Finnish (FIN)

AF:

0.0412

AC:

436

AN:

10594

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0723

AC:

4914

AN:

68006

Other (OTH)

AF:

0.0716

AC:

151

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

524

1047

1571

2094

2618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0740

Hom.:

Bravo

AF:

0.0756

Asia WGS

AF:

0.143

AC:

496

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.5

(source)

DANN

Benign

0.42

PhyloP100

0.18

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