dbSNP rs6081271: DTD1:c.477+14743T>C (chr20-18642976-T-C) – 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+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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

Publications

3 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=-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 rank	MANE	Protein	UniProt
DTD1	NM_080820.6 link	c.477+14743T>C		intron_variant	Intron 4 of 5	ENST00000377452.4	NP_543010.3	Q8TEA8
DUXAP7		n.18642976T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DTD1	ENST00000377452.4 link	c.477+14743T>C	intron_variant	Intron 4 of 5	1	NM_080820.6	ENSP00000366672.4	Q8TEA8
ENSG00000284776	ENST00000618693.4 link	c.552+14743T>C	intron_variant	Intron 4 of 4	5		ENSP00000482916.1	A0A087WZV9
DUXAP7	ENST00000431038.2 link	n.500-5A>G	splice_region_variant, intron_variant	Intron 1 of 1	6
DTD1	ENST00000647441.1 link	n.*140+14743T>C	intron_variant	Intron 5 of 6			ENSP00000493969.1	A0A2R8YCT7

Frequencies

GnomAD3 genomes

AF:

0.843

AC:

127422

AN:

151194

Hom.:

54539

Cov.:

show subpopulations

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.:

AF XY:

0.885

AC XY:

660

AN XY:

746

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.800

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.875

AC:

AN:

East Asian (EAS)

AF:

0.679

AC:

AN:

South Asian (SAS)

AF:

0.778

AC:

126

AN:

162

European-Finnish (FIN)

AF:

0.917

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.923

AC:

801

AN:

868

Other (OTH)

AF:

0.938

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

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:

0.843

AC:

127486

AN:

151310

Hom.:

54550

Cov.:

AF XY:

0.841

AC XY:

62183

AN XY:

73926

show subpopulations

African (AFR)

AF:

0.695

AC:

28571

AN:

41108

American (AMR)

AF:

0.831

AC:

12664

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.881

AC:

3055

AN:

3466

East Asian (EAS)

AF:

0.736

AC:

3783

AN:

5140

South Asian (SAS)

AF:

0.837

AC:

4016

AN:

4800

European-Finnish (FIN)

AF:

0.915

AC:

9503

AN:

10390

Middle Eastern (MID)

AF:

0.872

AC:

253

AN:

290

European-Non Finnish (NFE)

AF:

0.928

AC:

62965

AN:

67872

Other (OTH)

AF:

0.850

AC:

1783

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

807

1613

2420

3226

4033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.881

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

(source)

DANN

Benign

0.36

PhyloP100

-2.1

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