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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DTD1	NM_080820.6 link	c.477+14464C>G		intron_variant	Intron 4 of 5	ENST00000377452.4	NP_543010.3	Q8TEA8
DUXAP7		n.18642697C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DTD1	ENST00000377452.4 link	c.477+14464C>G	intron_variant	Intron 4 of 5	1	NM_080820.6	ENSP00000366672.4	Q8TEA8
ENSG00000284776	ENST00000618693.4 link	c.552+14464C>G	intron_variant	Intron 4 of 4	5		ENSP00000482916.1	A0A087WZV9
DTD1	ENST00000647441.1 link	n.*140+14464C>G	intron_variant	Intron 5 of 6			ENSP00000493969.1	A0A2R8YCT7
DUXAP7	ENST00000431038.2 link	n.*85G>C	downstream_gene_variant		6

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over