dbSNP rs138219395: MEG3:n.3015G>A (chr14-100836270-G-A) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The ENST00000398461.5(MEG3):n.3015G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0019 in 456,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0020 ( 0 hom. )

Consequence

MEG3
ENST00000398461.5 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

MEG3 (HGNC:14575): (maternally expressed 3) This gene is a maternally expressed imprinted gene. Multiple alternatively spliced transcript variants have been transcribed from this gene and all of them are long non-coding RNAs (lncRNAs). This gene is expressed in many normal tissues, but its expression is lost in multiple cancer cell lines of various tissue origins. It inhibits tumor cell proliferation in vitro. It also interacts with the tumor suppressor p53, and regulates p53 target gene expression. Its deletion enhances angiogenesis in vivo. Many experimental evidences demonstrate that this gene is a lncRNA tumor suppressor. [provided by RefSeq, Mar 2012]

MEG3 links:

MIR493HG (HGNC:55978): (MIR493 cluster host gene)

MIR493HG links:

ENSG00000258663 (HGNC:):

ENSG00000258663 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 14-100836270-G-A is Benign according to our data. Variant chr14-100836270-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3034727.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MEG3	NR_002766.2 link	n.1153G>A	non_coding_transcript_exon_variant	Exon 5 of 7
MEG3	NR_003530.2 link	n.1403G>A	non_coding_transcript_exon_variant	Exon 7 of 9
MEG3	NR_003531.3 link	n.1270G>A	non_coding_transcript_exon_variant	Exon 6 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MEG3	ENST00000398461.5 link	n.3015G>A	non_coding_transcript_exon_variant	Exon 2 of 4	1
MEG3	ENST00000429159.6 link	n.1169G>A	non_coding_transcript_exon_variant	Exon 5 of 7	1
MEG3	ENST00000451743.6 link	n.1135G>A	non_coding_transcript_exon_variant	Exon 5 of 7	1

Frequencies

GnomAD3 genomes

AF:

0.00166

AC:

252

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000785

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00322

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00197

AC:

275

AN:

139280

Hom.:

AF XY:

0.00183

AC XY:

138

AN XY:

75512

show subpopulations

Gnomad AFR exome

AF:

0.000155

Gnomad AMR exome

AF:

0.00316

Gnomad ASJ exome

AF:

0.000120

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000445

Gnomad FIN exome

AF:

0.000288

Gnomad NFE exome

AF:

0.00278

Gnomad OTH exome

AF:

0.00666

GnomAD4 exome

AF:

0.00202

AC:

615

AN:

304276

Hom.:

Cov.:

AF XY:

0.00186

AC XY:

323

AN XY:

173276

show subpopulations

Gnomad4 AFR exome

AF:

0.000116

Gnomad4 AMR exome

AF:

0.00345

Gnomad4 ASJ exome

AF:

0.0000927

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000586

Gnomad4 FIN exome

AF:

0.000391

Gnomad4 NFE exome

AF:

0.00286

Gnomad4 OTH exome

AF:

0.00169

GnomAD4 genome

AF:

0.00165

AC:

252

AN:

152302

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

109

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.000784

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00322

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00251

Hom.:

Bravo

AF:

0.00143

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MEG3-related disorder

Benign:1

Apr 05, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

DANN

Benign

0.70

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over