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rs2910164

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_029701.1(MIR146A):n.60C>G 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 0.727 in 528,390 control chromosomes in the GnomAD database, including 141,782 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 0.70 ( 38097 hom., cov: 31)
Exomes 𝑓: 0.74 ( 103685 hom. )

Consequence

MIR146A
NR_029701.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57
Variant links:
Genes affected
MIR3142HG (HGNC:51944): (MIR3142 host gene)
MIR146A (HGNC:31533): (microRNA 146a) 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. Some of the targets of the encoded miRNA are the transcripts for tumor necrosis factor, interleukin 1 receptor-associated kinase 1, interleukin 1-beta, TNF receptor-associated factor 6, and complement factor H. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR146ANR_029701.1 linkuse as main transcriptn.60C>G non_coding_transcript_exon_variant 1/1
MIR3142HGNR_132748.1 linkuse as main transcriptn.303C>G non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR3142HGENST00000517927.1 linkuse as main transcriptn.286C>G non_coding_transcript_exon_variant 2/21
MIR3142HGENST00000642173.1 linkuse as main transcriptn.189C>G non_coding_transcript_exon_variant 2/2
MIR146AENST00000385201.1 linkuse as main transcriptn.60C>G mature_miRNA_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.702
AC:
106630
AN:
151942
Hom.:
38071
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.607
Gnomad AMI
AF:
0.682
Gnomad AMR
AF:
0.708
Gnomad ASJ
AF:
0.783
Gnomad EAS
AF:
0.380
Gnomad SAS
AF:
0.705
Gnomad FIN
AF:
0.787
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.687
GnomAD3 exomes
AF:
0.713
AC:
175623
AN:
246292
Hom.:
64108
AF XY:
0.719
AC XY:
95733
AN XY:
133108
show subpopulations
Gnomad AFR exome
AF:
0.598
Gnomad AMR exome
AF:
0.694
Gnomad ASJ exome
AF:
0.777
Gnomad EAS exome
AF:
0.372
Gnomad SAS exome
AF:
0.720
Gnomad FIN exome
AF:
0.784
Gnomad NFE exome
AF:
0.770
Gnomad OTH exome
AF:
0.730
GnomAD4 exome
AF:
0.737
AC:
277348
AN:
376330
Hom.:
103685
Cov.:
0
AF XY:
0.738
AC XY:
157630
AN XY:
213566
show subpopulations
Gnomad4 AFR exome
AF:
0.599
Gnomad4 AMR exome
AF:
0.694
Gnomad4 ASJ exome
AF:
0.777
Gnomad4 EAS exome
AF:
0.376
Gnomad4 SAS exome
AF:
0.727
Gnomad4 FIN exome
AF:
0.782
Gnomad4 NFE exome
AF:
0.772
Gnomad4 OTH exome
AF:
0.733
GnomAD4 genome
AF:
0.702
AC:
106701
AN:
152060
Hom.:
38097
Cov.:
31
AF XY:
0.702
AC XY:
52221
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.607
Gnomad4 AMR
AF:
0.709
Gnomad4 ASJ
AF:
0.783
Gnomad4 EAS
AF:
0.380
Gnomad4 SAS
AF:
0.705
Gnomad4 FIN
AF:
0.787
Gnomad4 NFE
AF:
0.766
Gnomad4 OTH
AF:
0.688
Alfa
AF:
0.755
Hom.:
14093
Bravo
AF:
0.691
Asia WGS
AF:
0.549
AC:
1913
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
Cadd
Benign
17
Dann
Benign
0.76

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: rs2910164; hg19: chr5-159912418; API