Variant rs2648841 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_031613.1(MIR1208):n.72G>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 0.0417 in 510,780 control chromosomes in the GnomAD database, including 726 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 0.048 ( 267 hom., cov: 32)

Exomes 𝑓: 0.039 ( 459 hom. )

Consequence

MIR1208
NR_031613.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

MIR1208 (HGNC:35274): (microRNA 1208) 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]

MIR1208 links:

PVT1 (HGNC:9709): (Pvt1 oncogene) This gene represents a long non-coding RNA locus that has been identified as a candidate oncogene. Increased copy number and overexpression of this gene are associated with many types of cancers including breast and ovarian cancers, acute myeloid leukemia and Hodgkin lymphoma. Allelic variants of this gene are also associated with end-stage renal disease attributed to type 1 diabetes. Consistent with its association with various types of cancer, transcription of this gene is regulated by the tumor suppressor p53 through a canonical p53-binding site, and it has been implicated in regulating levels of the proto-oncogene MYC to promote tumorigenesis. [provided by RefSeq, Sep 2015]

PVT1 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1208	NR_031613.1 linkuse as main transcript	n.72G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR1208	ENST00000408334.1 linkuse as main transcript	n.72G>A	non_coding_transcript_exon_variant	1/1
PVT1	ENST00000651587.1 linkuse as main transcript	n.1378+2199G>A	intron_variant, non_coding_transcript_variant
PVT1	ENST00000650846.1 linkuse as main transcript	n.403+2199G>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

7263

AN:

152004

Hom.:

261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0956

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.0467

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.0540

Gnomad SAS

AF:

0.0714

Gnomad FIN

AF:

0.0287

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0198

Gnomad OTH

AF:

0.0407

GnomAD3 exomes

AF:

0.0422

AC:

9315

AN:

220756

Hom.:

299

AF XY:

0.0420

AC XY:

5100

AN XY:

121546

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.0689

Gnomad ASJ exome

AF:

0.0422

Gnomad EAS exome

AF:

0.0516

Gnomad SAS exome

AF:

0.0764

Gnomad FIN exome

AF:

0.0253

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0430

GnomAD4 exome

AF:

0.0391

AC:

14020

AN:

358658

Hom.:

459

Cov.:

AF XY:

0.0410

AC XY:

8442

AN XY:

205804

show subpopulations

Gnomad4 AFR exome

AF:

0.0989

Gnomad4 AMR exome

AF:

0.0679

Gnomad4 ASJ exome

AF:

0.0420

Gnomad4 EAS exome

AF:

0.0586

Gnomad4 SAS exome

AF:

0.0753

Gnomad4 FIN exome

AF:

0.0257

Gnomad4 NFE exome

AF:

0.0199

Gnomad4 OTH exome

AF:

0.0366

GnomAD4 genome

AF:

0.0480

AC:

7299

AN:

152122

Hom.:

267

Cov.:

AF XY:

0.0478

AC XY:

3554

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0961

Gnomad4 AMR

AF:

0.0466

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.0543

Gnomad4 SAS

AF:

0.0717

Gnomad4 FIN

AF:

0.0287

Gnomad4 NFE

AF:

0.0198

Gnomad4 OTH

AF:

0.0408

Alfa

AF:

0.0180

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.1

DANN

Benign

0.49

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