NM_080820.6:c.477+14960T>G

Variant names:

• chr20-18643193-T-G
• rs6132094
• NM_080820.6:c.477+14960T>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.477+14960T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 240,516 control chromosomes in the GnomAD database, including 32,565 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 0.51 (20070 hom., cov: 32)
  • Exomes 𝑓: 0.52 (12495 hom.)
• Consequence: DTD1 NM_080820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• 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:):

DUXAP7 (HGNC:32186): (double homeobox A pseudogene 7) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This pseudogene is a member of the DUXA homeobox gene family. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 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.477+14960T>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.477+14960T>G		intron	N/A	ENSP00000366672.4
	ENSG00000284776	ENST00000618693.4	TSL:5	c.552+14960T>G		intron	N/A	ENSP00000482916.1
	DUXAP7	ENST00000431038.2	TSL:6	n.442A>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77350 AN: 151906 Hom.: 20062 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.523 AC: 46289 AN: 88492 Hom.: 12495 Cov.: 0 AF XY: 0.518 AC XY: 25874 AN XY: 49944

African (AFR) AF: 0.480 AC: 1055 AN: 2200

American (AMR) AF: 0.495 AC: 4283 AN: 8644

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 1658 AN: 2476

East Asian (EAS) AF: 0.311 AC: 627 AN: 2018

South Asian (SAS) AF: 0.449 AC: 7594 AN: 16926

European-Finnish (FIN) AF: 0.524 AC: 2284 AN: 4358

Middle Eastern (MID) AF: 0.625 AC: 220 AN: 352

European-Non Finnish (NFE) AF: 0.557 AC: 26217 AN: 47098

Other (OTH) AF: 0.532 AC: 2351 AN: 4420

GnomAD4 genome AF: 0.509 AC: 77386 AN: 152024 Hom.: 20070 Cov.: 32 AF XY: 0.504 AC XY: 37427 AN XY: 74320

African (AFR) AF: 0.459 AC: 19006 AN: 41448

American (AMR) AF: 0.510 AC: 7798 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1616 AN: 5158

South Asian (SAS) AF: 0.410 AC: 1974 AN: 4820

European-Finnish (FIN) AF: 0.504 AC: 5317 AN: 10558

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37408 AN: 67968

Other (OTH) AF: 0.561 AC: 1186 AN: 2114

Alfa AF: 0.516 Hom.: 2586

Bravo AF: 0.507

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.51
PhyloP100		-0.80
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: rs6132094; hg19: chr20-18623837;