NM_080820.6:c.44-128G>A

Variant names:

• chr20-18593603-G-A
• rs6136423
• NM_080820.6:c.44-128G>A

Variant summary

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

The NM_080820.6(DTD1):​c.44-128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 664,860 control chromosomes in the GnomAD database, including 7,222 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 0.14 (1715 hom., cov: 32)
  • Exomes 𝑓: 0.14 (5507 hom.)
• Consequence: DTD1 NM_080820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.191 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.44-128G>A		intron	N/A	NP_543010.3
	DTD1	NM_001318043.2		c.44-128G>A		intron	N/A	NP_001304972.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTD1	ENST00000377452.4	TSL:1 MANE Select	c.44-128G>A		intron	N/A	ENSP00000366672.4
	ENSG00000284776	ENST00000618693.4	TSL:5	c.119-128G>A		intron	N/A	ENSP00000482916.1
	DTD1	ENST00000494921.2	TSL:2	c.44-128G>A		intron	N/A	ENSP00000495845.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22044 AN: 152016 Hom.: 1717 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.141 AC: 72206 AN: 512726 Hom.: 5507 AF XY: 0.136 AC XY: 37132 AN XY: 274034

African (AFR) AF: 0.127 AC: 1749 AN: 13788

American (AMR) AF: 0.208 AC: 5636 AN: 27140

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 2477 AN: 16352

East Asian (EAS) AF: 0.151 AC: 4535 AN: 30086

South Asian (SAS) AF: 0.0621 AC: 3359 AN: 54054

European-Finnish (FIN) AF: 0.162 AC: 7259 AN: 44772

Middle Eastern (MID) AF: 0.147 AC: 543 AN: 3688

European-Non Finnish (NFE) AF: 0.145 AC: 42788 AN: 295202

Other (OTH) AF: 0.140 AC: 3860 AN: 27644

GnomAD4 genome AF: 0.145 AC: 22050 AN: 152134 Hom.: 1715 Cov.: 32 AF XY: 0.146 AC XY: 10826 AN XY: 74378

African (AFR) AF: 0.127 AC: 5279 AN: 41522

American (AMR) AF: 0.197 AC: 3014 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.165 AC: 856 AN: 5180

South Asian (SAS) AF: 0.0555 AC: 267 AN: 4814

European-Finnish (FIN) AF: 0.166 AC: 1750 AN: 10570

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9761 AN: 67988

Other (OTH) AF: 0.161 AC: 341 AN: 2114

Alfa AF: 0.150 Hom.: 238

Bravo AF: 0.150

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.087
DANN	Benign	0.64
PhyloP100		-2.3
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: rs6136423; hg19: chr20-18574247;