chr1-168714262-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001937.5(DPT):c.390T>C(p.Phe130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,614,048 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00081 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 3 hom. )
Consequence
DPT
NM_001937.5 synonymous
NM_001937.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.756
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 1-168714262-A-G is Benign according to our data. Variant chr1-168714262-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 726434.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.756 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPT | NM_001937.5 | c.390T>C | p.Phe130= | synonymous_variant | 2/4 | ENST00000367817.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPT | ENST00000367817.4 | c.390T>C | p.Phe130= | synonymous_variant | 2/4 | 1 | NM_001937.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000809 AC: 123AN: 152060Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000995 AC: 250AN: 251312Hom.: 0 AF XY: 0.00109 AC XY: 148AN XY: 135818
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GnomAD4 exome AF: 0.00115 AC: 1680AN: 1461870Hom.: 3 Cov.: 31 AF XY: 0.00121 AC XY: 877AN XY: 727238
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GnomAD4 genome ? AF: 0.000808 AC: 123AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000806 AC XY: 60AN XY: 74398
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 01, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at