Variant chr12-126144376-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 ENST00000643016.1(LINC02359):n.495-10820T>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 0.501 in 152,080 control chromosomes in the GnomAD database, including 19,870 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 0.50 ( 19870 hom., cov: 33)

Consequence

LINC02359
ENST00000643016.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.35

Variant links:

Genes affected

LINC02359 (HGNC:53280): (long intergenic non-protein coding RNA 2359)

LINC02359 links:

LOC107984447 (HGNC:):

LOC107984447 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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984447	XR_001749374.2 linkuse as main transcript	n.490+8738A>G		intron_variant, non_coding_transcript_variant
LOC107984447	XR_001749373.2 linkuse as main transcript	n.490+8738A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02359	ENST00000643016.1 linkuse as main transcript	n.495-10820T>C	intron_variant, non_coding_transcript_variant
LINC02359	ENST00000653935.1 linkuse as main transcript	n.218-10820T>C	intron_variant, non_coding_transcript_variant
LINC02359	ENST00000654753.1 linkuse as main transcript	n.608-10820T>C	intron_variant, non_coding_transcript_variant
LINC02359	ENST00000658727.1 linkuse as main transcript	n.438-10820T>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

76129

AN:

151962

Hom.:

19831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.808

Gnomad SAS

AF:

0.526

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.481

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

GnomAD4 genome

AF:

0.501

AC:

76228

AN:

152080

Hom.:

19870

Cov.:

AF XY:

0.501

AC XY:

37253

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.586

Gnomad4 AMR

AF:

0.484

Gnomad4 ASJ

AF:

0.375

Gnomad4 EAS

AF:

0.808

Gnomad4 SAS

AF:

0.526

Gnomad4 FIN

AF:

0.431

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.471

Hom.:

2150

Bravo

AF:

0.507

Asia WGS

AF:

0.655

AC:

2277

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

0.86

DANN

Benign

0.28

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