rs11231898

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000413053.2(MIR194-2HG):​n.1843C>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

MIR194-2HG
ENST00000413053.2 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)
MIR192 (HGNC:31562): (microRNA 192) 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 was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
MIR194-2NR_029829.1 linkn.76C>T non_coding_transcript_exon_variant Exon 1 of 1
MIR194-2HGNR_133638.1 linkn.1843C>T non_coding_transcript_exon_variant Exon 2 of 2
MIR194-2HGNR_133639.1 linkn.437+1065C>T intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR194-2ENST00000384864.1 linkn.76C>T non_coding_transcript_exon_variant Exon 1 of 1 6
MIR194-2HGENST00000413053.2 linkn.1843C>T non_coding_transcript_exon_variant Exon 2 of 2 2
MIR194-2HGENST00000710929.1 linkn.390+1226C>T intron_variant Intron 3 of 3

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
GnomAD2 exomes
AF:
0.00484
AC:
1090
AN:
225156
AF XY:
0.00353
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 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
AC:
684
AN:
10326
Gnomad4 AMR exome
AF:
0.00363
AC:
126
AN:
34682
Gnomad4 ASJ exome
AF:
0.00237
AC:
27
AN:
11376
Gnomad4 EAS exome
AF:
0.000238
AC:
3
AN:
12594
Gnomad4 SAS exome
AF:
0.0000619
AC:
4
AN:
64598
Gnomad4 FIN exome
AF:
0.00
AC:
0
AN:
30668
Gnomad4 NFE exome
AF:
0.000178
AC:
33
AN:
185876
Gnomad4 Remaining exome
AF:
0.00336
AC:
54
AN:
16088
Heterozygous variant carriers
0
43
85
128
170
213
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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
AC:
0.0642416
AN:
0.0642416
Gnomad4 AMR
AF:
0.00778
AC:
0.00778286
AN:
0.00778286
Gnomad4 ASJ
AF:
0.00173
AC:
0.0017311
AN:
0.0017311
Gnomad4 EAS
AF:
0.000581
AC:
0.000580945
AN:
0.000580945
Gnomad4 SAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.000294
AC:
0.000294196
AN:
0.000294196
Gnomad4 OTH
AF:
0.0147
AC:
0.014678
AN:
0.014678
Heterozygous variant carriers
0
124
248
373
497
621
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
28
56
84
112
140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00610
Hom.:
33
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