GeneBe

ENST00000427348.5:n.111+847T>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000427348.5(MIR663AHG):​n.111+847T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MIR663AHG
ENST00000427348.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Publications

0 publications found
Variant links:
Genes affected
MIR663AHG (HGNC:27662): (MIR663A host gene)
MIR663A (HGNC:32919): (microRNA 663a) 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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR663ANR_030386.1 linkn.3T>A non_coding_transcript_exon_variant Exon 1 of 1
MIR663AHGNR_040095.1 linkn.111+847T>A intron_variant Intron 1 of 4
MIR663Aunassigned_transcript_3435 n.-12T>A upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR663AHGENST00000427348.5 linkn.111+847T>A intron_variant Intron 1 of 4 1
MIR663AENST00000385250.1 linkn.3T>A non_coding_transcript_exon_variant Exon 1 of 1 6
MIR663AHGENST00000432499.6 linkn.41+723T>A intron_variant Intron 1 of 4 5

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
138554
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
82612
African (AFR)
AF:
0.00
AC:
0
AN:
2400
American (AMR)
AF:
0.00
AC:
0
AN:
10166
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
5738
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1252
South Asian (SAS)
AF:
0.00
AC:
0
AN:
31132
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6834
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
992
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
73798
Other (OTH)
AF:
0.00
AC:
0
AN:
6242
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
6.6
DANN
Benign
0.70
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs7266947; hg19: chr20-26188912; API