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GeneBe

1-168696573-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001937.5(DPT):c.582C>T(p.Tyr194=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,613,920 control chromosomes in the GnomAD database, including 364 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 183 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 181 hom. )

Consequence

DPT
NM_001937.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.731
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-168696573-G-A is Benign according to our data. Variant chr1-168696573-G-A is described in ClinVar as [Benign]. Clinvar id is 789696.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.731 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DPTNM_001937.5 linkuse as main transcriptc.582C>T p.Tyr194= synonymous_variant 4/4 ENST00000367817.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DPTENST00000367817.4 linkuse as main transcriptc.582C>T p.Tyr194= synonymous_variant 4/41 NM_001937.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0266
AC:
4049
AN:
152102
Hom.:
184
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0920
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0106
Gnomad ASJ
AF:
0.00317
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000338
Gnomad OTH
AF:
0.0191
GnomAD3 exomes
AF:
0.00731
AC:
1837
AN:
251190
Hom.:
98
AF XY:
0.00556
AC XY:
755
AN XY:
135762
show subpopulations
Gnomad AFR exome
AF:
0.0975
Gnomad AMR exome
AF:
0.00533
Gnomad ASJ exome
AF:
0.00169
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000294
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000220
Gnomad OTH exome
AF:
0.00310
GnomAD4 exome
AF:
0.00279
AC:
4076
AN:
1461700
Hom.:
181
Cov.:
31
AF XY:
0.00238
AC XY:
1730
AN XY:
727156
show subpopulations
Gnomad4 AFR exome
AF:
0.0955
Gnomad4 AMR exome
AF:
0.00575
Gnomad4 ASJ exome
AF:
0.00176
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000371
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000147
Gnomad4 OTH exome
AF:
0.00601
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0266
AC:
4056
AN:
152220
Hom.:
183
Cov.:
33
AF XY:
0.0261
AC XY:
1946
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.0919
Gnomad4 AMR
AF:
0.0106
Gnomad4 ASJ
AF:
0.00317
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000338
Gnomad4 OTH
AF:
0.0189
Alfa
AF:
0.00192
Hom.:
12
Bravo
AF:
0.0309
Asia WGS
AF:
0.00491
AC:
17
AN:
3478
EpiCase
AF:
0.000382
EpiControl
AF:
0.000474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
2.9
Dann
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.15
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12060879; hg19: chr1-168665811; API