NM_152544.3:c.1131+529G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152544.3(TRMT44):c.1131+529G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,452 control chromosomes in the GnomAD database, including 16,979 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 0.46 ( 16945 hom., cov: 33)
Exomes 𝑓: 0.40 ( 34 hom. )
Consequence
TRMT44
NM_152544.3 intron
NM_152544.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.516
Publications
3 publications found
Genes affected
TRMT44 (HGNC:26653): (tRNA methyltransferase 44 homolog) The protein encoded by this gene is a putative tRNA methyltransferase found in the cytoplasm. Defects in this gene may be a cause of partial epilepsy with pericentral spikes (PEPS), but that has not been proven definitively. [provided by RefSeq, May 2012]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRMT44 | ENST00000389737.5 | c.1131+529G>A | intron_variant | Intron 5 of 10 | 5 | NM_152544.3 | ENSP00000374387.4 | |||
TRMT44 | ENST00000513449.6 | c.408+529G>A | intron_variant | Intron 5 of 8 | 1 | ENSP00000424643.2 | ||||
ENSG00000251186 | ENST00000515186.1 | n.556C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.465 AC: 70669AN: 151922Hom.: 16949 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
70669
AN:
151922
Hom.:
Cov.:
33
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: 0.398 AC: 164AN: 412Hom.: 34 Cov.: 0 AF XY: 0.412 AC XY: 98AN XY: 238 show subpopulations
GnomAD4 exome
AF:
AC:
164
AN:
412
Hom.:
Cov.:
0
AF XY:
AC XY:
98
AN XY:
238
show subpopulations
African (AFR)
AF:
AC:
3
AN:
8
American (AMR)
AF:
AC:
2
AN:
8
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
2
East Asian (EAS)
AF:
AC:
1
AN:
6
South Asian (SAS)
AF:
AC:
12
AN:
16
European-Finnish (FIN)
AF:
AC:
0
AN:
6
Middle Eastern (MID)
AF:
AC:
3
AN:
4
European-Non Finnish (NFE)
AF:
AC:
140
AN:
350
Other (OTH)
AF:
AC:
2
AN:
12
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.484
Heterozygous variant carriers
0
4
8
13
17
21
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<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: 0.465 AC: 70683AN: 152040Hom.: 16945 Cov.: 33 AF XY: 0.469 AC XY: 34871AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
70683
AN:
152040
Hom.:
Cov.:
33
AF XY:
AC XY:
34871
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
15072
AN:
41462
American (AMR)
AF:
AC:
6629
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
1675
AN:
3468
East Asian (EAS)
AF:
AC:
2721
AN:
5168
South Asian (SAS)
AF:
AC:
3229
AN:
4820
European-Finnish (FIN)
AF:
AC:
5525
AN:
10574
Middle Eastern (MID)
AF:
AC:
158
AN:
294
European-Non Finnish (NFE)
AF:
AC:
34276
AN:
67960
Other (OTH)
AF:
AC:
980
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1940
3881
5821
7762
9702
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
672
1344
2016
2688
3360
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2010
AN:
3478
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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