Variant chr2-207269271-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 NR_146973.1(LINC01802):n.316+378T>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 0.189 in 532,310 control chromosomes in the GnomAD database, including 12,340 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 0.24 ( 6030 hom., cov: 32)

Exomes 𝑓: 0.17 ( 6310 hom. )

Consequence

LINC01802
NR_146973.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Variant links:

Genes affected

(HGNC:):

links:

LINC01802 (HGNC:52591): (long intergenic non-protein coding RNA 1802)

LINC01802 links:

MIR1302-4 (HGNC:35296): (microRNA 1302-4) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1302-4 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01802	NR_146973.1 linkuse as main transcript	n.316+378T>C		intron_variant, non_coding_transcript_variant
MIR1302-4	NR_031633.1 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
	ENST00000412387.5 linkuse as main transcript	n.316-28933A>G	intron_variant, non_coding_transcript_variant	4
LINC01802	ENST00000438824.1 linkuse as main transcript	n.316+378T>C	intron_variant, non_coding_transcript_variant	3
MIR1302-4	ENST00000408701.1 linkuse as main transcript		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36291

AN:

152036

Hom.:

6022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.0943

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.214

GnomAD3 exomes

AF:

0.180

AC:

44292

AN:

245688

Hom.:

4979

AF XY:

0.174

AC XY:

23286

AN XY:

133720

show subpopulations

Gnomad AFR exome

AF:

0.472

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.148

Gnomad EAS exome

AF:

0.163

Gnomad SAS exome

AF:

0.195

Gnomad FIN exome

AF:

0.0891

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.160

GnomAD4 exome

AF:

0.169

AC:

64388

AN:

380156

Hom.:

6310

Cov.:

AF XY:

0.168

AC XY:

36337

AN XY:

216576

show subpopulations

Gnomad4 AFR exome

AF:

0.472

Gnomad4 AMR exome

AF:

0.227

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.0961

Gnomad4 NFE exome

AF:

0.147

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.239

AC:

36335

AN:

152154

Hom.:

6030

Cov.:

AF XY:

0.235

AC XY:

17464

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.466

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.139

Gnomad4 EAS

AF:

0.176

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.0943

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.197

Hom.:

1984

Bravo

AF:

0.258

Asia WGS

AF:

0.189

AC:

659

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.014

DANN

Benign

0.27

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