Menu
GeneBe

rs11231898

Variant summary

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

The NR_029829.1(MIR194-2):n.76C>T 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 0.00725 in 521,136 control chromosomes in the GnomAD database, including 139 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 0.019 ( 106 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 33 hom. )

Consequence

MIR194-2
NR_029829.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.758
Variant links:
Genes affected
MIR194-2 (HGNC:31565): (microRNA 194-2) 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]
MIR194-2HG (HGNC:51946): (MIR194-2 host gene)

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=-0.6).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0622 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR194-2NR_029829.1 linkuse as main transcriptn.76C>T non_coding_transcript_exon_variant 1/1
MIR194-2HGNR_133640.1 linkuse as main transcriptn.276+1226C>T intron_variant, non_coding_transcript_variant
MIR194-2HGNR_133638.1 linkuse as main transcriptn.1843C>T non_coding_transcript_exon_variant 2/2
MIR194-2HGNR_133639.1 linkuse as main transcriptn.437+1065C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR194-2ENST00000384864.1 linkuse as main transcriptn.76C>T non_coding_transcript_exon_variant 1/1
MIR194-2HGENST00000710930.1 linkuse as main transcriptn.551+1065C>T intron_variant, non_coding_transcript_variant
MIR194-2HGENST00000413053.2 linkuse as main transcriptn.1843C>T non_coding_transcript_exon_variant 2/22
MIR194-2HGENST00000710929.1 linkuse as main transcriptn.390+1226C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0187
AC:
2838
AN:
152014
Hom.:
106
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0643
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00779
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.000580
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0148
GnomAD3 exomes
AF:
0.00484
AC:
1090
AN:
225156
Hom.:
32
AF XY:
0.00353
AC XY:
432
AN XY:
122504
show subpopulations
Gnomad AFR exome
AF:
0.0654
Gnomad AMR exome
AF:
0.00360
Gnomad ASJ exome
AF:
0.00265
Gnomad EAS exome
AF:
0.000469
Gnomad SAS exome
AF:
0.0000713
Gnomad FIN exome
AF:
0.0000524
Gnomad NFE exome
AF:
0.000261
Gnomad OTH exome
AF:
0.00252
GnomAD4 exome
AF:
0.00254
AC:
936
AN:
369004
Hom.:
33
Cov.:
0
AF XY:
0.00187
AC XY:
393
AN XY:
209762
show subpopulations
Gnomad4 AFR exome
AF:
0.0662
Gnomad4 AMR exome
AF:
0.00363
Gnomad4 ASJ exome
AF:
0.00237
Gnomad4 EAS exome
AF:
0.000238
Gnomad4 SAS exome
AF:
0.0000619
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000178
Gnomad4 OTH exome
AF:
0.00336
GnomAD4 genome
AF:
0.0187
AC:
2844
AN:
152132
Hom.:
106
Cov.:
32
AF XY:
0.0176
AC XY:
1311
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.0642
Gnomad4 AMR
AF:
0.00778
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.000581
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.0147
Alfa
AF:
0.00560
Hom.:
29
Bravo
AF:
0.0209
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
Cadd
Benign
6.4
Dann
Benign
0.88

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: rs11231898; hg19: chr11-64658836; API