rs41276930

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000384970.1(MIR7-2):n.18C>T 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 0.00664 in 519,372 control chromosomes in the GnomAD database, including 53 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 0.0049 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0073 ( 48 hom. )

Consequence

MIR7-2
ENST00000384970.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.67

Publications

10 publications found

Variant links:

Genes affected

MIR7-2 (HGNC:31639): (microRNA 7-2) 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]

MIR7-2 links:

AEN (HGNC:25722): (apoptosis enhancing nuclease) Enables exonuclease activity. Involved in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator and response to ionizing radiation. Located in nuclear membrane; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

AEN links:

MIR3529 (HGNC:41564): (microRNA 3529) 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]

MIR3529 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
MIR7-2	NR_029606.1 link	n.18C>T	non_coding_transcript_exon_variant	Exon 1 of 1
AEN	XM_017022489.2 link	c.-65+3000C>T	intron_variant	Intron 2 of 4	XP_016877978.1
AEN	XM_047432946.1 link	c.-65+3000C>T	intron_variant	Intron 2 of 4	XP_047288902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR7-2	ENST00000384970.1 link	n.18C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR3529	ENST00000637713.1 link	n.*5G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.00495

AC:

752

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00406

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.0377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00301

Gnomad OTH

AF:

0.00287

GnomAD2 exomes

AF:

0.00661

AC:

1520

AN:

230030

AF XY:

0.00731

show subpopulations

Gnomad AFR exome

AF:

0.000349

Gnomad AMR exome

AF:

0.00176

Gnomad ASJ exome

AF:

0.000629

Gnomad EAS exome

AF:

0.000123

Gnomad FIN exome

AF:

0.0352

Gnomad NFE exome

AF:

0.00310

Gnomad OTH exome

AF:

0.00873

GnomAD4 exome

AF:

0.00735

AC:

2698

AN:

367182

Hom.:

Cov.:

AF XY:

0.00782

AC XY:

1638

AN XY:

209456

show subpopulations

African (AFR)

AF:

0.000624

AC:

AN:

9618

American (AMR)

AF:

0.00163

AC:

AN:

34286

Ashkenazi Jewish (ASJ)

AF:

0.000704

AC:

AN:

11358

East Asian (EAS)

AF:

0.0000861

AC:

AN:

11610

South Asian (SAS)

AF:

0.0138

AC:

889

AN:

64190

European-Finnish (FIN)

AF:

0.0349

AC:

1112

AN:

31872

Middle Eastern (MID)

AF:

0.00886

AC:

AN:

2032

European-Non Finnish (NFE)

AF:

0.00255

AC:

475

AN:

186118

Other (OTH)

AF:

0.00826

AC:

133

AN:

16098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

125

250

376

501

626

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.00493

AC:

750

AN:

152190

Hom.:

Cov.:

AF XY:

0.00671

AC XY:

499

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.000409

AC:

AN:

41534

American (AMR)

AF:

0.00406

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.000577

AC:

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5174

South Asian (SAS)

AF:

0.0108

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0377

AC:

400

AN:

10600

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00301

AC:

205

AN:

67994

Other (OTH)

AF:

0.00284

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

103

138

172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00293

Hom.:

Bravo

AF:

0.00194

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.5

(source)

DANN

Benign

0.84

PhyloP100

-2.7

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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