1-100146375-A-G

Variant names:

• chr1-100146375-A-G
• rs506044
• NM_019083.3:c.818-1519A>G

Variant summary

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

The NM_019083.3(TRMT13):​c.818-1519A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,214 control chromosomes in the GnomAD database, including 45,376 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 0.75 (45376 hom., cov: 33)
• Consequence: TRMT13 NM_019083.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

TRMT13 (HGNC:25502): (tRNA methyltransferase 13 homolog) Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT13	NM_019083.3	c.818-1519A>G		intron_variant	Intron 9 of 10	ENST00000370141.8	NP_061956.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT13	ENST00000370141.8	c.818-1519A>G		intron_variant	Intron 9 of 10	1	NM_019083.3	ENSP00000359160.2

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113994 AN: 152096 Hom.: 45364 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.749 AC: 114033 AN: 152214 Hom.: 45376 Cov.: 33 AF XY: 0.756 AC XY: 56261 AN XY: 74434

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.787

Alfa AF: 0.828 Hom.: 24075

Bravo AF: 0.735

Asia WGS AF: 0.869 AC: 3021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.7
DANN	Benign	0.88

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: rs506044; hg19: chr1-100611931;