dbSNP rs2631753: TRMT44:c.1131+529G>A (chr4-8453518-G-A) – ACMG Classification: Benign (-12 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.516

Publications

3 publications found

Variant links:

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]

TRMT44 links:

ENSG00000251186 (HGNC:58729):

ENSG00000251186 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_152544.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152544.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT44	NM_152544.3	MANE Select	c.1131+529G>A		intron	N/A	NP_689757.2	Q8IYL2-1
	TRMT44	NM_001350233.2		c.408+529G>A		intron	N/A	NP_001337162.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TRMT44	ENST00000389737.5	TSL:5 MANE Select	c.1131+529G>A	intron	N/A	ENSP00000374387.4	Q8IYL2-1
TRMT44	ENST00000513449.6	TSL:1	c.408+529G>A	intron	N/A	ENSP00000424643.2	Q8IYL2-2
TRMT44	ENST00000905717.1		c.1254+406G>A	intron	N/A	ENSP00000575776.1

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70669

AN:

151922

Hom.:

16949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.364

Gnomad AMI

AF:

0.461

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.398

AC:

164

AN:

412

Hom.:

Cov.:

AF XY:

0.412

AC XY:

AN XY:

238

show subpopulations

African (AFR)

AF:

0.375

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

140

AN:

350

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

70683

AN:

152040

Hom.:

16945

Cov.:

AF XY:

0.469

AC XY:

34871

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.364

AC:

15072

AN:

41462

American (AMR)

AF:

0.434

AC:

6629

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.483

AC:

1675

AN:

3468

East Asian (EAS)

AF:

0.527

AC:

2721

AN:

5168

South Asian (SAS)

AF:

0.670

AC:

3229

AN:

4820

European-Finnish (FIN)

AF:

0.523

AC:

5525

AN:

10574

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.504

AC:

34276

AN:

67960

Other (OTH)

AF:

0.464

AC:

980

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

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

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:

0.477

Hom.:

7589

Bravo

AF:

0.447

Asia WGS

AF:

0.579

AC:

2010

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.87

(source)

DANN

Benign

0.57

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over