rs1357482

Variant names:

• chr4-8494956-G-A
• rs1357482
• ENST00000528132.1:n.170+12517G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528132.1(ENSG00000205959):​n.170+12517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,276 control chromosomes in the GnomAD database, including 494 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 0.060 (494 hom., cov: 32)
• Consequence: ENSG00000205959 ENST00000528132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 publications found

Genes affected

ENSG00000205959 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT44	XM_047449679.1	c.2045-13842G>A		intron_variant	Intron 10 of 11		XP_047305635.1
TRMT44	XM_047449680.1	c.2045-13842G>A		intron_variant	Intron 10 of 12		XP_047305636.1
TRMT44	XM_047449681.1	c.2045-13842G>A		intron_variant	Intron 10 of 10		XP_047305637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000205959	ENST00000528132.1	n.170+12517G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9035 AN: 152158 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0595 AC: 9063 AN: 152276 Hom.: 494 Cov.: 32 AF XY: 0.0571 AC XY: 4249 AN XY: 74462

African (AFR) AF: 0.144 AC: 5973 AN: 41540

American (AMR) AF: 0.0300 AC: 459 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4830

European-Finnish (FIN) AF: 0.0143 AC: 152 AN: 10622

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0320 AC: 2175 AN: 68014

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0528 Hom.: 68

Bravo AF: 0.0643

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.79
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1357482; hg19: chr4-8496683;