rs524705
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001937.5(DPT):c.540-121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 831,300 control chromosomes in the GnomAD database, including 137,053 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 0.61 ( 29837 hom., cov: 30)
Exomes 𝑓: 0.56 ( 107216 hom. )
Consequence
DPT
NM_001937.5 intron
NM_001937.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.687
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPT | NM_001937.5 | c.540-121A>G | intron_variant | ENST00000367817.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPT | ENST00000367817.4 | c.540-121A>G | intron_variant | 1 | NM_001937.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.614 AC: 93180AN: 151806Hom.: 29787 Cov.: 30
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GnomAD4 exome AF: 0.556 AC: 377673AN: 679374Hom.: 107216 AF XY: 0.557 AC XY: 197252AN XY: 354080
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GnomAD4 genome ? AF: 0.614 AC: 93288AN: 151926Hom.: 29837 Cov.: 30 AF XY: 0.612 AC XY: 45464AN XY: 74232
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at