Variant rs4666488 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000641932.1(LINC01808):n.945G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 152,180 control chromosomes in the GnomAD database, including 711 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 0.061 ( 711 hom., cov: 32)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

LINC01808
ENST00000641932.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.155

Variant links:

Genes affected

LINC01808 (HGNC:52611): (long intergenic non-protein coding RNA 1808)

LINC01808 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=-0.62).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LINC01808	NR_183418.1 link	n.484-980G>A	intron_variant
LINC01808	NR_183419.1 link	n.423-980G>A	intron_variant
LINC01808	NR_183420.1 link	n.423-980G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC01808	ENST00000641932.1 link	n.945G>A	non_coding_transcript_exon_variant	5/7
LINC01808	ENST00000666694.1 link	n.398G>A	non_coding_transcript_exon_variant	4/5
LINC01808	ENST00000450628.2 link	n.355-980G>A	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0608

AC:

9246

AN:

152048

Hom.:

713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0634

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0216

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0602

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0195

Gnomad OTH

AF:

0.0458

GnomAD4 exome

AF:

0.0714

AC:

AN:

Hom.:

Cov.:

AF XY:

0.125

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.100

GnomAD4 genome

AF:

0.0608

AC:

9246

AN:

152166

Hom.:

711

Cov.:

AF XY:

0.0683

AC XY:

5078

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0632

Gnomad4 AMR

AF:

0.110

Gnomad4 ASJ

AF:

0.0216

Gnomad4 EAS

AF:

0.392

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0602

Gnomad4 NFE

AF:

0.0195

Gnomad4 OTH

AF:

0.0463

Alfa

AF:

0.0354

Hom.:

Bravo

AF:

0.0638

Asia WGS

AF:

0.240

AC:

832

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

8.8

DANN

Benign

0.85

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