rs10904887

Variant names:

• chr10-17146642-T-A
• rs10904887
• ENST00000354631.7:n.*3594A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-17146642-T-A
• chr10-17146642-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000354631.7(TRDMT1):​n.*3594A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRDMT1 ENST00000354631.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 11 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000354631.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRDMT1	NM_004412.7	MANE Select	c.*2398A>T		3_prime_UTR	Exon 11 of 11	NP_004403.1
	TRDMT1	NM_001351219.2		c.*2398A>T		3_prime_UTR	Exon 11 of 11	NP_001338148.1
	TRDMT1	NM_001351221.2		c.*2398A>T		3_prime_UTR	Exon 9 of 9	NP_001338150.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRDMT1	ENST00000354631.7	TSL:1	n.*3594A>T		non_coding_transcript_exon	Exon 12 of 12	ENSP00000346652.3
	TRDMT1	ENST00000377799.8	TSL:1 MANE Select	c.*2398A>T		3_prime_UTR	Exon 11 of 11	ENSP00000367030.3
	TRDMT1	ENST00000354631.7	TSL:1	n.*3594A>T		3_prime_UTR	Exon 12 of 12	ENSP00000346652.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.6
DANN	Benign	0.77
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs10904887; hg19: chr10-17188641;