Genetic Variant DPT:p.Thr80Thr (chr1-168728935-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001937.5(DPT):c.240G>A(p.Thr80Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,613,916 control chromosomes in the GnomAD database, including 204,390 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 0.43 ( 15462 hom., cov: 32)

Exomes 𝑓: 0.50 ( 188928 hom. )

Consequence

DPT
NM_001937.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.42

Publications

18 publications found

Variant links:

Genes affected

DPT (HGNC:3011): (dermatopontin) Dermatopontin is an extracellular matrix protein with possible functions in cell-matrix interactions and matrix assembly. The protein is found in various tissues and many of its tyrosine residues are sulphated. Dermatopontin is postulated to modify the behavior of TGF-beta through interaction with decorin. [provided by RefSeq, Jul 2008]

DPT links:

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

LINC00970 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-5.42 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPT	NM_001937.5 link	c.240G>A	p.Thr80Thr	synonymous_variant	Exon 1 of 4	ENST00000367817.4	NP_001928.2	Q07507

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPT	ENST00000367817.4 link	c.240G>A	p.Thr80Thr	synonymous_variant	Exon 1 of 4	1	NM_001937.5	ENSP00000356791.3		Q07507

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65993

AN:

151920

Hom.:

15465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.830

Gnomad AMR

AF:

0.367

Gnomad ASJ

AF:

0.560

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.444

GnomAD2 exomes

AF:

0.427

AC:

107125

AN:

250962

AF XY:

0.435

show subpopulations

Gnomad AFR exome

AF:

0.308

Gnomad AMR exome

AF:

0.263

Gnomad ASJ exome

AF:

0.555

Gnomad EAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.462

GnomAD4 exome

AF:

0.499

AC:

730028

AN:

1461878

Hom.:

188928

Cov.:

AF XY:

0.497

AC XY:

361119

AN XY:

727240

show subpopulations

African (AFR)

AF:

0.299

AC:

10027

AN:

33480

American (AMR)

AF:

0.274

AC:

12274

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

14586

AN:

26136

East Asian (EAS)

AF:

0.178

AC:

7062

AN:

39700

South Asian (SAS)

AF:

0.363

AC:

31299

AN:

86258

European-Finnish (FIN)

AF:

0.477

AC:

25472

AN:

53420

Middle Eastern (MID)

AF:

0.391

AC:

2258

AN:

5768

European-Non Finnish (NFE)

AF:

0.539

AC:

598920

AN:

1111996

Other (OTH)

AF:

0.466

AC:

28130

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

22651

45301

67952

90602

113253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16660

33320

49980

66640

83300

<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:

0.434

AC:

65997

AN:

152038

Hom.:

15462

Cov.:

AF XY:

0.426

AC XY:

31637

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.309

AC:

12803

AN:

41438

American (AMR)

AF:

0.366

AC:

5594

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.560

AC:

1941

AN:

3468

East Asian (EAS)

AF:

0.164

AC:

845

AN:

5168

South Asian (SAS)

AF:

0.359

AC:

1735

AN:

4830

European-Finnish (FIN)

AF:

0.456

AC:

4825

AN:

10576

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.536

AC:

36450

AN:

67960

Other (OTH)

AF:

0.443

AC:

936

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1833

3667

5500

7334

9167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.484

Hom.:

53932

Bravo

AF:

0.417

Asia WGS

AF:

0.265

AC:

922

AN:

3478

EpiCase

AF:

0.526

EpiControl

AF:

0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.11

(source)

DANN

Benign

0.81

PhyloP100

-5.4

PromoterAI

-0.014

Neutral

(source)

Mutation Taster

=98/2

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