dbSNP rs6132093: DTD1:c.477+14464C>G (chr20-18642697-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080820.6(DTD1):c.477+14464C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,098 control chromosomes in the GnomAD database, including 19,973 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 ( 19934 hom., cov: 31)

Exomes 𝑓: 0.59 ( 39 hom. )

Consequence

DTD1
NM_080820.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.520

Publications

2 publications found

Variant links:

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 links:

ENSG00000284776 (HGNC:):

ENSG00000284776 links:

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]

DUXAP7 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTD1	NM_080820.6	MANE Select	c.477+14464C>G		intron	N/A	NP_543010.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DTD1	ENST00000377452.4	TSL:1 MANE Select	c.477+14464C>G	intron	N/A	ENSP00000366672.4	Q8TEA8
ENSG00000284776	ENST00000618693.4	TSL:5	c.552+14464C>G	intron	N/A	ENSP00000482916.1	A0A087WZV9
DTD1	ENST00000916788.1		c.477+14464C>G	intron	N/A	ENSP00000586847.1

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

77064

AN:

151758

Hom.:

19926

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.509

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.562

GnomAD4 exome

AF:

0.595

AC:

132

AN:

222

Hom.:

AF XY:

0.627

AC XY:

AN XY:

142

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.613

AC:

AN:

160

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.508

AC:

77100

AN:

151876

Hom.:

19934

Cov.:

AF XY:

0.502

AC XY:

37262

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.458

AC:

18945

AN:

41406

American (AMR)

AF:

0.509

AC:

7764

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.664

AC:

2306

AN:

3472

East Asian (EAS)

AF:

0.312

AC:

1604

AN:

5144

South Asian (SAS)

AF:

0.409

AC:

1971

AN:

4820

European-Finnish (FIN)

AF:

0.503

AC:

5293

AN:

10532

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.549

AC:

37268

AN:

67934

Other (OTH)

AF:

0.558

AC:

1174

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1880

3760

5640

7520

9400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.526

Hom.:

2650

Bravo

AF:

0.506

Asia WGS

AF:

0.344

AC:

1197

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.0

(source)

DANN

Benign

0.77

PhyloP100

0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over