ENST00000699461.1:n.496+3789C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000699461.1(MEG9):n.496+3789C>T variant causes a intron 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Publications

13 publications found

Variant links:

Genes affected

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

MEG9 links:

MIR412 (HGNC:32064): (microRNA 412) 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]

MIR412 links:

MIR369 (HGNC:31783): (microRNA 369) 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]

MIR369 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect
MIR369	NR_029862.1 link	n.-202C>T	upstream_gene_variant
MIR412	NR_030155.1 link	n.-51C>T	upstream_gene_variant
MIR412	unassigned_transcript_2446	n.-69C>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MEG9	ENST00000699461.1 link	n.496+3789C>T	intron_variant	Intron 4 of 6
MEG9	ENST00000699462.1 link	n.219+1029C>T	intron_variant	Intron 1 of 3
MEG9	ENST00000818609.1 link	n.258+1029C>T	intron_variant	Intron 1 of 1

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

GnomAD2 exomes

AF:

0.0329

AC:

8254

AN:

251060

AF XY:

0.0335

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 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

African (AFR)

AF:

0.0102

AC:

106

AN:

10432

American (AMR)

AF:

0.0170

AC:

617

AN:

36250

Ashkenazi Jewish (ASJ)

AF:

0.0895

AC:

1048

AN:

11706

East Asian (EAS)

AF:

0.00

AC:

AN:

12994

South Asian (SAS)

AF:

0.0158

AC:

1054

AN:

66692

European-Finnish (FIN)

AF:

0.0250

AC:

808

AN:

32294

Middle Eastern (MID)

AF:

0.0592

AC:

168

AN:

2836

European-Non Finnish (NFE)

AF:

0.0458

AC:

8607

AN:

187988

Other (OTH)

AF:

0.0418

AC:

692

AN:

16540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

867

1735

2602

3470

4337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0308

AC:

4685

AN:

152234

Hom.:

134

Cov.:

AF XY:

0.0292

AC XY:

2171

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.00842

AC:

350

AN:

41550

American (AMR)

AF:

0.0273

AC:

417

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0880

AC:

305

AN:

3464

East Asian (EAS)

AF:

0.000194

AC:

AN:

5166

South Asian (SAS)

AF:

0.0131

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0231

AC:

245

AN:

10614

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0463

AC:

3151

AN:

68008

Other (OTH)

AF:

0.0365

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

222

443

665

886

1108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0420

Hom.:

225

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

(source)

DANN

Benign

0.95

PhyloP100

0.19

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over