Variant rs1002486 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000659779.1(LINC01811):n.379-86708A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,586 control chromosomes in the GnomAD database, including 5,127 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 0.23 ( 5127 hom., cov: 32)

Consequence

LINC01811
ENST00000659779.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.576

Variant links:

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

LINC01811 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01811	ENST00000659779.1 linkuse as main transcript	n.379-86708A>C		intron_variant, non_coding_transcript_variant
LINC01811	ENST00000669904.1 linkuse as main transcript	n.240-86708A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35291

AN:

151468

Hom.:

5120

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.0812

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.212

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

GnomAD4 genome

AF:

0.233

AC:

35328

AN:

151586

Hom.:

5127

Cov.:

AF XY:

0.237

AC XY:

17553

AN XY:

74060

show subpopulations

Gnomad4 AFR

AF:

0.371

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.0812

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.158

Hom.:

3116

Bravo

AF:

0.252

Asia WGS

AF:

0.276

AC:

957

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.6

DANN

Benign

0.67

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