20-18738217-T-G

Variant names:

• chr20-18738217-T-G
• rs6075409
• NM_080820.6:c.478-5883T>G

Variant summary

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

The NM_080820.6(DTD1):​c.478-5883T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,200 control chromosomes in the GnomAD database, including 1,622 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 0.13 (1622 hom., cov: 33)
• Consequence: DTD1 NM_080820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 3 publications found

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]

ENSG00000284776 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080820.6. 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
	DTD1	NM_080820.6	MANE Select	c.478-5883T>G		intron	N/A	NP_543010.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTD1	ENST00000377452.4	TSL:1 MANE Select	c.478-5883T>G		intron	N/A	ENSP00000366672.4
	ENSG00000284776	ENST00000618693.4	TSL:5	c.553-5883T>G		intron	N/A	ENSP00000482916.1
	DTD1	ENST00000647441.1		n.*141-5883T>G		intron	N/A	ENSP00000493969.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19956 AN: 152082 Hom.: 1623 Cov.: 33

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0635

Gnomad EAS AF: 0.0639

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.131 AC: 19953 AN: 152200 Hom.: 1622 Cov.: 33 AF XY: 0.135 AC XY: 10060 AN XY: 74414

African (AFR) AF: 0.0442 AC: 1837 AN: 41544

American (AMR) AF: 0.107 AC: 1635 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0635 AC: 220 AN: 3466

East Asian (EAS) AF: 0.0633 AC: 328 AN: 5180

South Asian (SAS) AF: 0.184 AC: 886 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10580

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12141 AN: 67990

Other (OTH) AF: 0.108 AC: 228 AN: 2114

Alfa AF: 0.152 Hom.: 1045

Bravo AF: 0.116

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6075409; hg19: chr20-18718861;