Variant 9-90304862-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000425666.2(LINC01508):n.339-3209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,020 control chromosomes in the GnomAD database, including 14,298 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 0.42 ( 14298 hom., cov: 32)

Consequence

LINC01508
ENST00000425666.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Variant links:

Genes affected

LINC01508 (HGNC:51190): (long intergenic non-protein coding RNA 1508)

LINC01508 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01508	NR_109795.1 link	n.262-3209A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01508	ENST00000425666.2 link	n.339-3209A>G	intron_variant	3
LINC01508	ENST00000436671.2 link	n.979-3209A>G	intron_variant	3
LINC01508	ENST00000659218.1 link	n.402-3209A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63925

AN:

151902

Hom.:

14273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.503

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.344

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.421

AC:

64004

AN:

152020

Hom.:

14298

Cov.:

AF XY:

0.422

AC XY:

31399

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.554

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.268

Gnomad4 EAS

AF:

0.588

Gnomad4 SAS

AF:

0.503

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.339

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.358

Hom.:

17166

Bravo

AF:

0.429

Asia WGS

AF:

0.574

AC:

1995

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.2

DANN

Benign

0.73

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