chr4-99554903-C-T

Variant summary

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

The NM_001134665.3(TRMT10A):​c.496-969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,952 control chromosomes in the GnomAD database, including 30,238 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 0.59 ( 30238 hom., cov: 31)

Consequence

TRMT10A
NM_001134665.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79
Variant links:
Genes affected
TRMT10A (HGNC:28403): (tRNA methyltransferase 10A) This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRMT10ANM_001134665.3 linkuse as main transcriptc.496-969G>A intron_variant ENST00000394876.7 NP_001128137.1 Q8TBZ6V9HVY8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRMT10AENST00000394876.7 linkuse as main transcriptc.496-969G>A intron_variant 1 NM_001134665.3 ENSP00000378342.2 Q8TBZ6

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90286
AN:
151834
Hom.:
30196
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.608
Gnomad AMR
AF:
0.472
Gnomad ASJ
AF:
0.704
Gnomad EAS
AF:
0.771
Gnomad SAS
AF:
0.617
Gnomad FIN
AF:
0.305
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.463
Gnomad OTH
AF:
0.600
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.595
AC:
90369
AN:
151952
Hom.:
30238
Cov.:
31
AF XY:
0.588
AC XY:
43683
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.895
Gnomad4 AMR
AF:
0.471
Gnomad4 ASJ
AF:
0.704
Gnomad4 EAS
AF:
0.771
Gnomad4 SAS
AF:
0.613
Gnomad4 FIN
AF:
0.305
Gnomad4 NFE
AF:
0.463
Gnomad4 OTH
AF:
0.603
Alfa
AF:
0.500
Hom.:
9382
Bravo
AF:
0.617
Asia WGS
AF:
0.645
AC:
2238
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.036
DANN
Benign
0.41

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1491233; hg19: chr4-100476060; API