dbSNP rs4467881: ENSG00000286380:n.432-6898C>T (chr7-129770304-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000710872.1(ENSG00000286380):n.432-6898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 437,738 control chromosomes in the GnomAD database, including 64,838 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 0.56 ( 24652 hom., cov: 32)

Exomes 𝑓: 0.51 ( 40186 hom. )

Consequence

ENSG00000286380
ENST00000710872.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0670

Publications

7 publications found

Variant links:

COSMIC-nc: COSV63012826

Genes affected

ENSG00000286380 (HGNC:):

ENSG00000286380 links:

MIR182 (HGNC:31553): (microRNA 182) 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]

MIR182 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR182	NR_029614.1 link	n.*79C>T	downstream_gene_variant
MIR182	unassigned_transcript_1304	n.*102C>T	downstream_gene_variant
MIR182	unassigned_transcript_1305	n.*143C>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286380	ENST00000710872.1 link	n.432-6898C>T		intron_variant	Intron 1 of 1
MIR182	ENST00000385255.3 link	n.*79C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.559

AC:

84923

AN:

151900

Hom.:

24633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.598

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.0666

Gnomad SAS

AF:

0.397

Gnomad FIN

AF:

0.502

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.551

GnomAD4 exome

AF:

0.515

AC:

147086

AN:

285720

Hom.:

40186

AF XY:

0.507

AC XY:

80534

AN XY:

158968

show subpopulations

African (AFR)

AF:

0.586

AC:

4838

AN:

8256

American (AMR)

AF:

0.427

AC:

12314

AN:

28842

Ashkenazi Jewish (ASJ)

AF:

0.653

AC:

5512

AN:

8446

East Asian (EAS)

AF:

0.0456

AC:

439

AN:

9634

South Asian (SAS)

AF:

0.408

AC:

22775

AN:

55860

European-Finnish (FIN)

AF:

0.504

AC:

10326

AN:

20502

Middle Eastern (MID)

AF:

0.625

AC:

651

AN:

1042

European-Non Finnish (NFE)

AF:

0.593

AC:

83198

AN:

140330

Other (OTH)

AF:

0.549

AC:

7033

AN:

12808

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

3235

6470

9706

12941

16176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.559

AC:

84983

AN:

152018

Hom.:

24652

Cov.:

AF XY:

0.550

AC XY:

40889

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.598

AC:

24807

AN:

41452

American (AMR)

AF:

0.507

AC:

7759

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.654

AC:

2271

AN:

3470

East Asian (EAS)

AF:

0.0670

AC:

346

AN:

5166

South Asian (SAS)

AF:

0.398

AC:

1917

AN:

4822

European-Finnish (FIN)

AF:

0.502

AC:

5307

AN:

10576

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.599

AC:

40662

AN:

67922

Other (OTH)

AF:

0.545

AC:

1149

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1863

3726

5589

7452

9315

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

714

1428

2142

2856

3570

<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:

0.589

Hom.:

5352

Bravo

AF:

0.557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.5

(source)

DANN

Benign

0.80

PhyloP100

-0.067

Mutation Taster

=99/1

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