Variant rs61992670 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000699461.1(MEG9):n.496+3789C>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 0.0336 in 529,966 control chromosomes in the GnomAD database, including 456 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 0.031 ( 134 hom., cov: 32)

Exomes 𝑓: 0.035 ( 322 hom. )

Consequence

MEG9
ENST00000699461.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Variant links:

Genes affected

MEG9 (HGNC:43874): (maternally expressed 9)

MEG9 links:

MIR409 (HGNC:32055): (microRNA 409) 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]

MIR409 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=-0.54).

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR409	NR_029975.1 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect
MEG9	ENST00000699461.1 linkuse as main transcript	n.496+3789C>T	intron_variant, non_coding_transcript_variant
MEG9	ENST00000699462.1 linkuse as main transcript	n.219+1029C>T	intron_variant, non_coding_transcript_variant
MIR409	ENST00000362237.3 linkuse as main transcript		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0308

AC:

4683

AN:

152116

Hom.:

134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00845

Gnomad AMI

AF:

0.0703

Gnomad AMR

AF:

0.0271

Gnomad ASJ

AF:

0.0880

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0130

Gnomad FIN

AF:

0.0231

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0463

Gnomad OTH

AF:

0.0373

GnomAD3 exomes

AF:

0.0329

AC:

8254

AN:

251060

Hom.:

194

AF XY:

0.0335

AC XY:

4547

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00938

Gnomad AMR exome

AF:

0.0175

Gnomad ASJ exome

AF:

0.0902

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0154

Gnomad FIN exome

AF:

0.0231

Gnomad NFE exome

AF:

0.0475

Gnomad OTH exome

AF:

0.0367

GnomAD4 exome

AF:

0.0347

AC:

13100

AN:

377732

Hom.:

322

Cov.:

AF XY:

0.0336

AC XY:

7199

AN XY:

214222

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

Gnomad4 AMR exome

AF:

0.0170

Gnomad4 ASJ exome

AF:

0.0895

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0158

Gnomad4 FIN exome

AF:

0.0250

Gnomad4 NFE exome

AF:

0.0458

Gnomad4 OTH exome

AF:

0.0418

GnomAD4 genome

AF:

0.0308

AC:

4685

AN:

152234

Hom.:

134

Cov.:

AF XY:

0.0292

AC XY:

2171

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00842

Gnomad4 AMR

AF:

0.0273

Gnomad4 ASJ

AF:

0.0880

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0131

Gnomad4 FIN

AF:

0.0231

Gnomad4 NFE

AF:

0.0463

Gnomad4 OTH

AF:

0.0365

Alfa

AF:

0.0438

Hom.:

Bravo

AF:

0.0305

Asia WGS

AF:

0.00491

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.95

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