Genetic Variant LINC01787:n.166-10663A>T (chr1-96315001-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435311.1(LINC01787):n.166-10663A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,000 control chromosomes in the GnomAD database, including 1,127 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 ( 1127 hom., cov: 32)

Consequence

LINC01787
ENST00000435311.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.483

Publications

3 publications found

Variant links:

Genes affected

LINC01787 (HGNC:52576): (long intergenic non-protein coding RNA 1787)

LINC01787 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01787	NR_110693.1 link	n.166-10663A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01787	ENST00000435311.1 link	n.166-10663A>T		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17892

AN:

151882

Hom.:

1130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.118

AC:

17888

AN:

152000

Hom.:

1127

Cov.:

AF XY:

0.116

AC XY:

8594

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.130

AC:

5406

AN:

41472

American (AMR)

AF:

0.102

AC:

1545

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

651

AN:

3468

East Asian (EAS)

AF:

0.00212

AC:

AN:

5186

South Asian (SAS)

AF:

0.169

AC:

815

AN:

4818

European-Finnish (FIN)

AF:

0.0802

AC:

850

AN:

10604

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8161

AN:

67922

Other (OTH)

AF:

0.129

AC:

272

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

766

1533

2299

3066

3832

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.115

Hom.:

119

Bravo

AF:

0.119

Asia WGS

AF:

0.0770

AC:

269

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.0030

(source)

DANN

Benign

0.12

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism

(source)

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