Variant chr6-24746511-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_183315.1(LINC02828):n.43-2485C>T 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 0.107 in 151,890 control chromosomes in the GnomAD database, including 1,081 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 0.11 ( 1081 hom., cov: 32)

Consequence

LINC02828
NR_183315.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.352

Variant links:

Genes affected

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

LINC02828 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02828	NR_183315.1 linkuse as main transcript	n.43-2485C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02828	ENST00000665572.1 linkuse as main transcript	n.268-2485C>T	intron_variant, non_coding_transcript_variant
LINC02828	ENST00000423504.2 linkuse as main transcript	n.49-2485C>T	intron_variant, non_coding_transcript_variant	2
LINC02828	ENST00000453179.1 linkuse as main transcript	n.46-2485C>T	intron_variant, non_coding_transcript_variant	4
LINC02828	ENST00000668439.1 linkuse as main transcript	n.238-5052C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16286

AN:

151772

Hom.:

1081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0328

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.0795

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.0889

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

GnomAD4 genome

AF:

0.107

AC:

16285

AN:

151890

Hom.:

1081

Cov.:

AF XY:

0.106

AC XY:

7902

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.0327

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.0797

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.0880

Alfa

AF:

0.128

Hom.:

498

Bravo

AF:

0.105

Asia WGS

AF:

0.0820

AC:

284

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

DANN

Benign

0.60

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