rs10516192

Positions:

• chr4-8462083-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152544.3(TRMT44):​c.1204-1902A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,356 control chromosomes in the GnomAD database, including 96 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 0.026 (96 hom., cov: 33)
• Consequence: TRMT44 NM_152544.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRMT44	NM_152544.3	c.1204-1902A>C		intron_variant		ENST00000389737.5	NP_689757.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRMT44	ENST00000389737.5	c.1204-1902A>C		intron_variant		5	NM_152544.3	ENSP00000374387.4
TRMT44	ENST00000513449.6	c.481-1902A>C		intron_variant		1		ENSP00000424643.2
TRMT44	ENST00000532477.1	n.228-1902A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 3960 AN: 152238 Hom.: 93 Cov.: 33

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00982

Gnomad OTH AF: 0.0244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0262 AC: 3985 AN: 152356 Hom.: 96 Cov.: 33 AF XY: 0.0262 AC XY: 1952 AN XY: 74498

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0335

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00982

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0196 Hom.: 10

Bravo AF: 0.0281

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.024
DANN	Benign	0.72

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

Other links and lift over

dbSNP: rs10516192; hg19: chr4-8463810;