rs6081271

Positions:

• chr20-18642976-T-C

Variant summary

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

The NM_080820.6(DTD1):​c.477+14743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,556 control chromosomes in the GnomAD database, including 55,051 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 0.84 (54550 hom., cov: 28)
  • Exomes 𝑓: 0.89 (501 hom.)
• Consequence: DTD1 NM_080820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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

Verdict is Benign. Variant got -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 = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTD1	NM_080820.6	c.477+14743T>C		intron_variant		ENST00000377452.4	NP_543010.3
DUXAP7		n.18642976T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTD1	ENST00000377452.4	c.477+14743T>C		intron_variant		1	NM_080820.6	ENSP00000366672.4
ENSG00000284776	ENST00000618693.4	c.552+14743T>C		intron_variant		5		ENSP00000482916.1
DUXAP7	ENST00000431038.2	n.500-5A>G		splice_region_variant, intron_variant		6
DTD1	ENST00000647441.1	n.*140+14743T>C		intron_variant				ENSP00000493969.1

Frequencies

GnomAD3 genomes AF: 0.843 AC: 127422 AN: 151194 Hom.: 54539 Cov.: 28

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.875

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.855

GnomAD4 exome AF: 0.893 AC: 1113 AN: 1246 Hom.: 501 Cov.: 0 AF XY: 0.885 AC XY: 660 AN XY: 746

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.800

Gnomad4 ASJ exome AF: 0.875

Gnomad4 EAS exome AF: 0.679

Gnomad4 SAS exome AF: 0.778

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.923

Gnomad4 OTH exome AF: 0.938

GnomAD4 genome AF: 0.843 AC: 127486 AN: 151310 Hom.: 54550 Cov.: 28 AF XY: 0.841 AC XY: 62183 AN XY: 73926

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.850

Alfa AF: 0.881 Hom.: 7434

Bravo AF: 0.826

Asia WGS AF: 0.750 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.36

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: rs6081271; hg19: chr20-18623620;