dbSNP rs1425419: LINC01091:n.546-7978C>T (chr4-123644809-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 ENST00000662928.1(LINC01091):n.546-7978C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,136 control chromosomes in the GnomAD database, including 2,786 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 0.16 ( 2786 hom., cov: 31)

Consequence

LINC01091
ENST00000662928.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Publications

4 publications found

Variant links:

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

LINC01091 links:

ENSG00000304190 (HGNC:):

ENSG00000304190 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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01091	ENST00000662928.1 link	n.546-7978C>T	intron_variant	Intron 1 of 3
LINC01091	ENST00000664622.1 link	n.212-7982C>T	intron_variant	Intron 1 of 8
LINC01091	ENST00000666328.1 link	n.637-7978C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24422

AN:

152018

Hom.:

2792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0419

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.160

AC:

24405

AN:

152136

Hom.:

2786

Cov.:

AF XY:

0.174

AC XY:

12906

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0417

AC:

1733

AN:

41552

American (AMR)

AF:

0.296

AC:

4524

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

650

AN:

3470

East Asian (EAS)

AF:

0.334

AC:

1725

AN:

5160

South Asian (SAS)

AF:

0.356

AC:

1714

AN:

4818

European-Finnish (FIN)

AF:

0.269

AC:

2842

AN:

10564

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10721

AN:

67982

Other (OTH)

AF:

0.151

AC:

319

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1006

2012

3018

4024

5030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.158

Hom.:

4035

Bravo

AF:

0.154

Asia WGS

AF:

0.271

AC:

944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.7

(source)

DANN

Benign

0.69

PhyloP100

0.21

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