Variant 6-24749185-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.195+37C>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 0.103 in 152,202 control chromosomes in the GnomAD database, including 956 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 0.10 ( 954 hom., cov: 32)

Exomes 𝑓: 0.14 ( 2 hom. )

Consequence

LINC02828
NR_183315.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

Variant links:

Genes affected

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

LINC02828 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02828	NR_183315.1 linkuse as main transcript	n.195+37C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02828	ENST00000665572.1 linkuse as main transcript	n.420+37C>T	intron_variant, non_coding_transcript_variant
LINC02828	ENST00000423504.2 linkuse as main transcript	n.201+37C>T	intron_variant, non_coding_transcript_variant	2
LINC02828	ENST00000453179.1 linkuse as main transcript	n.198+37C>T	intron_variant, non_coding_transcript_variant	4
LINC02828	ENST00000668439.1 linkuse as main transcript	n.238-2378C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15614

AN:

152042

Hom.:

954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0529

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.0815

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.00655

Gnomad SAS

AF:

0.0598

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.143

AC:

AN:

Hom.:

Cov.:

AF XY:

0.176

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.103

AC:

15618

AN:

152160

Hom.:

954

Cov.:

AF XY:

0.102

AC XY:

7570

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0530

Gnomad4 AMR

AF:

0.0813

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.00657

Gnomad4 SAS

AF:

0.0600

Gnomad4 FIN

AF:

0.150

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.128

Hom.:

1771

Bravo

AF:

0.0987

Asia WGS

AF:

0.0350

AC:

122

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.91

DANN

Benign

0.81

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