rs2631753

chr4-8453518-G-Achr4-8453518-G-Cchr4-8453518-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT44	NM_152544.3	c.1131+529G>A		intron_variant		ENST00000389737.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT44	ENST00000389737.5	c.1131+529G>A		intron_variant		5	NM_152544.3	P2
TRMT44	ENST00000513449.6	c.408+529G>A		intron_variant		1		A2
	ENST00000515186.1	n.556C>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70669 AN: 151922 Hom.: 16949 Cov.: 33

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.: 34 Cov.: 0 AF XY: 0.412 AC XY: 98 AN XY: 238

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.465 AC: 70683 AN: 152040 Hom.: 16945 Cov.: 33 AF XY: 0.469 AC XY: 34871 AN XY: 74300

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.464

Alfa AF: 0.476 Hom.: 6598

Bravo AF: 0.447

Asia WGS AF: 0.579 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.87
Dann	Benign	0.57

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: rs2631753; hg19: chr4-8455245;