chr10-17162188-G-A

Variant names:

• chr10-17162188-G-A
• rs11254413
• NM_004412.7:c.301C>T

Variant summary

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

The NM_004412.7(TRDMT1):​c.301C>T​(p.His101Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,604,150 control chromosomes in the GnomAD database, including 160,429 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (14372 hom., cov: 27)
  • Exomes 𝑓: 0.44 (146057 hom.)
• Consequence: TRDMT1 NM_004412.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 44 publications found

Genes affected

TRDMT1 (HGNC:2977): (tRNA aspartic acid methyltransferase 1) This gene encodes a protein responsible for the methylation of aspartic acid transfer RNA, specifically at the cytosine-38 residue in the anticodon loop. This enzyme also possesses residual DNA-(cytosine-C5) methyltransferase activity. While similar in sequence and structure to DNA cytosine methyltransferases, this gene is distinct and highly conserved in its function among taxa. [provided by RefSeq, Jun 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=3.259778E-4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004412.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRDMT1	NM_004412.7	MANE Select	c.301C>T	p.His101Tyr	missense	Exon 4 of 11	NP_004403.1	O14717-1
	TRDMT1	NM_001351219.2		c.301C>T	p.His101Tyr	missense	Exon 4 of 11	NP_001338148.1
	TRDMT1	NM_001351220.2		c.301C>T	p.His101Tyr	missense	Exon 4 of 11	NP_001338149.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRDMT1	ENST00000377799.8	TSL:1 MANE Select	c.301C>T	p.His101Tyr	missense	Exon 4 of 11	ENSP00000367030.3	O14717-1
	TRDMT1	ENST00000436968.6	TSL:1	c.109-1814C>T		intron	N/A	ENSP00000390611.2	H0Y4A2
	TRDMT1	ENST00000354631.7	TSL:1	n.*321C>T		non_coding_transcript_exon	Exon 5 of 12	ENSP00000346652.3	Q7Z3E4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65189 AN: 149850 Hom.: 14355 Cov.: 27

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.458

GnomAD2 exomes AF: 0.410 AC: 101539 AN: 247550 AF XY: 0.413

Gnomad AFR exome AF: 0.419

Gnomad AMR exome AF: 0.359

Gnomad ASJ exome AF: 0.395

Gnomad EAS exome AF: 0.239

Gnomad FIN exome AF: 0.431

Gnomad NFE exome AF: 0.467

Gnomad OTH exome AF: 0.424

GnomAD4 exome AF: 0.445 AC: 646854 AN: 1454184 Hom.: 146057 Cov.: 33 AF XY: 0.443 AC XY: 320318 AN XY: 723496

African (AFR) AF: 0.421 AC: 13895 AN: 33030

American (AMR) AF: 0.362 AC: 15990 AN: 44202

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 10232 AN: 25976

East Asian (EAS) AF: 0.227 AC: 8930 AN: 39348

South Asian (SAS) AF: 0.355 AC: 30345 AN: 85360

European-Finnish (FIN) AF: 0.433 AC: 23072 AN: 53250

Middle Eastern (MID) AF: 0.427 AC: 2447 AN: 5734

European-Non Finnish (NFE) AF: 0.466 AC: 515762 AN: 1107212

Other (OTH) AF: 0.436 AC: 26181 AN: 60072

GnomAD4 genome AF: 0.435 AC: 65223 AN: 149966 Hom.: 14372 Cov.: 27 AF XY: 0.429 AC XY: 31361 AN XY: 73152

African (AFR) AF: 0.424 AC: 17241 AN: 40644

American (AMR) AF: 0.403 AC: 6081 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1429 AN: 3458

East Asian (EAS) AF: 0.249 AC: 1258 AN: 5044

South Asian (SAS) AF: 0.360 AC: 1707 AN: 4742

European-Finnish (FIN) AF: 0.428 AC: 4282 AN: 10014

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31459 AN: 67694

Other (OTH) AF: 0.461 AC: 966 AN: 2094

Alfa AF: 0.452 Hom.: 59243

Bravo AF: 0.433

TwinsUK AF: 0.457 AC: 1694

ALSPAC AF: 0.462 AC: 1779

ESP6500AA AF: 0.431 AC: 1898

ESP6500EA AF: 0.453 AC: 3897

ExAC AF: 0.417 AC: 50690

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.047
BayesDel_addAF	Benign	-0.58	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	0.39
DANN	Benign	0.20
DEOGEN2	Uncertain	0.62	D
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.010	N
LIST_S2	Benign	0.42	T
MetaRNN	Benign	0.00033	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.22	N
PhyloP100		0.55
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-1.5	N
REVEL	Benign	0.083
Sift	Benign	0.76	T
Sift4G	Benign	0.44	T
Polyphen		0.011	B
Vest4		0.17
MPC		0.017
ClinPred		0.0022	T
GERP RS		-2.1
Varity_R		0.27
gMVP		0.74
Mutation Taster		=95/5	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11254413; hg19: chr10-17204187; COSMIC: COSV58318669;