20-18676957-C-T

Variant summary

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

The NM_080820.6(DTD1):c.477+48724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,996 control chromosomes in the GnomAD database, including 10,264 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 0.36 (10264 hom., cov: 32)
• Consequence: DTD1 NM_080820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

DTD1 (HGNC:16219): (D-aminoacyl-tRNA deacylase 1) The protein encoded by this gene is similar in sequence to histidyl-tRNA synthetase, which hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). The encoded protein binds the DNA unwinding element and plays a role in the initiation of DNA replication. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

DTD1-AS1 (HGNC:40762): (DTD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DTD1	NM_080820.6	c.477+48724C>T		intron_variant		ENST00000377452.4
DTD1-AS1	NR_109955.1	n.475-1343G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DTD1	ENST00000377452.4	c.477+48724C>T		intron_variant		1	NM_080820.6	P1
DTD1-AS1	ENST00000428285.1	n.476-1343G>A		intron_variant, non_coding_transcript_variant		1
DTD1	ENST00000647441.1	c.*140+48724C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54967 AN: 151878 Hom.: 10256 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.362 AC: 54999 AN: 151996 Hom.: 10264 Cov.: 32 AF XY: 0.356 AC XY: 26431 AN XY: 74268

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.397

Alfa AF: 0.267 Hom.: 905

Bravo AF: 0.354

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.70

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: rs6132097; hg19: chr20-18657601;