chr1-170151574-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136107.2(NTMT2):c.154+5313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 153,176 control chromosomes in the GnomAD database, including 84 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 0.027 ( 82 hom., cov: 31)
Exomes 𝑓: 0.012 ( 2 hom. )
Consequence
NTMT2
NM_001136107.2 intron
NM_001136107.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.68
Publications
2 publications found
Genes affected
NTMT2 (HGNC:31932): (N-terminal Xaa-Pro-Lys N-methyltransferase 2) Enables N-terminal protein N-methyltransferase activity. Involved in N-terminal protein amino acid methylation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
MIR3119-1 (HGNC:38253): (microRNA 3119-1) 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]
MIR3119-2 (HGNC:38315): (microRNA 3119-2) 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]
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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=-0.94).
BA1
GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTMT2 | ENST00000439373.3 | c.154+5313T>C | intron_variant | Intron 1 of 3 | 1 | NM_001136107.2 | ENSP00000408058.3 | |||
MIR3119-1 | ENST00000637673.1 | n.-112A>G | upstream_gene_variant | 6 | ||||||
MIR3119-2 | ENST00000577602.1 | n.*112T>C | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0273 AC: 4149AN: 151988Hom.: 82 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
4149
AN:
151988
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0121 AC: 13AN: 1070Hom.: 2 AF XY: 0.0101 AC XY: 6AN XY: 596 show subpopulations
GnomAD4 exome
AF:
AC:
13
AN:
1070
Hom.:
AF XY:
AC XY:
6
AN XY:
596
show subpopulations
African (AFR)
AF:
AC:
0
AN:
28
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
0
AN:
24
European-Finnish (FIN)
AF:
AC:
8
AN:
402
Middle Eastern (MID)
AF:
AC:
1
AN:
536
European-Non Finnish (NFE)
AF:
AC:
3
AN:
14
Other (OTH)
AF:
AC:
1
AN:
66
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.469
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0273 AC: 4152AN: 152106Hom.: 82 Cov.: 31 AF XY: 0.0255 AC XY: 1897AN XY: 74340 show subpopulations
GnomAD4 genome
AF:
AC:
4152
AN:
152106
Hom.:
Cov.:
31
AF XY:
AC XY:
1897
AN XY:
74340
show subpopulations
African (AFR)
AF:
AC:
334
AN:
41572
American (AMR)
AF:
AC:
245
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
91
AN:
3470
East Asian (EAS)
AF:
AC:
49
AN:
5094
South Asian (SAS)
AF:
AC:
226
AN:
4802
European-Finnish (FIN)
AF:
AC:
319
AN:
10604
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
2829
AN:
67956
Other (OTH)
AF:
AC:
55
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
202
404
606
808
1010
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
149
AN:
3472
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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