rs940136

Variant names:

• chr4-8447265-G-A
• rs940136
• NM_152544.3:c.734+675G>A

Variant summary

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

The NM_152544.3(TRMT44):​c.734+675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,148 control chromosomes in the GnomAD database, including 39,113 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 0.71 (39113 hom., cov: 33)
• Consequence: TRMT44 NM_152544.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT44	NM_152544.3	c.734+675G>A		intron_variant	Intron 2 of 10	ENST00000389737.5	NP_689757.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT44	ENST00000389737.5	c.734+675G>A		intron_variant	Intron 2 of 10	5	NM_152544.3	ENSP00000374387.4
TRMT44	ENST00000513449.6	c.40+675G>A		intron_variant	Intron 2 of 8	1		ENSP00000424643.2
TRMT44	ENST00000504134.1	c.479-2433G>A		intron_variant	Intron 1 of 1	3		ENSP00000434207.1
TRMT44	ENST00000528167.1	n.752+675G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107808 AN: 152030 Hom.: 39062 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.709 AC: 107909 AN: 152148 Hom.: 39113 Cov.: 33 AF XY: 0.706 AC XY: 52520 AN XY: 74378

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.700

Alfa AF: 0.677 Hom.: 16180

Bravo AF: 0.705

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.54

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: rs940136; hg19: chr4-8448992;