3-67225635-G-T

Variant summary

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

The NR_036234.1(MIR4272):​n.*108G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 153,476 control chromosomes in the GnomAD database, including 69,502 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 0.95 ( 68957 hom., cov: 33)
Exomes 𝑓: 0.97 ( 545 hom. )

Consequence

MIR4272
NR_036234.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670
Variant links:
Genes affected
MIR4272 (HGNC:38303): (microRNA 4272) 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR4272NR_036234.1 linkn.*108G>T downstream_gene_variant
MIR4272unassigned_transcript_639 n.*118G>T downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR4272ENST00000635924.1 linkn.*108G>T downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.951
AC:
144674
AN:
152200
Hom.:
68896
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.899
Gnomad AMI
AF:
0.979
Gnomad AMR
AF:
0.926
Gnomad ASJ
AF:
0.928
Gnomad EAS
AF:
0.959
Gnomad SAS
AF:
0.987
Gnomad FIN
AF:
0.993
Gnomad MID
AF:
0.943
Gnomad NFE
AF:
0.979
Gnomad OTH
AF:
0.945
GnomAD4 exome
AF:
0.971
AC:
1123
AN:
1156
Hom.:
545
AF XY:
0.974
AC XY:
641
AN XY:
658
show subpopulations
Gnomad4 AFR exome
AF:
0.844
Gnomad4 AMR exome
AF:
1.00
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.991
Gnomad4 NFE exome
AF:
0.973
Gnomad4 OTH exome
AF:
0.933
GnomAD4 genome
AF:
0.951
AC:
144795
AN:
152320
Hom.:
68957
Cov.:
33
AF XY:
0.953
AC XY:
70948
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.899
Gnomad4 AMR
AF:
0.926
Gnomad4 ASJ
AF:
0.928
Gnomad4 EAS
AF:
0.959
Gnomad4 SAS
AF:
0.987
Gnomad4 FIN
AF:
0.993
Gnomad4 NFE
AF:
0.979
Gnomad4 OTH
AF:
0.946
Alfa
AF:
0.955
Hom.:
11721
Bravo
AF:
0.940
Asia WGS
AF:
0.980
AC:
3408
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.51
DANN
Benign
0.44

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.

Other links and lift over

dbSNP: rs9868022; hg19: chr3-67276059; API