dbSNP rs1425419: LINC01091:n.546-7978C>T (chr4-123644809-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

LINC01091 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR

AF:

0.0417

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.334

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.269

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.158

Hom.:

2868

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

DANN

Benign

0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over