rs61731008
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_014208.3(DSPP):c.303C>T(p.Asn101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,613,532 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0039 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00070 ( 4 hom. )
Consequence
DSPP
NM_014208.3 synonymous
NM_014208.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.37
Genes affected
DSPP (HGNC:3054): (dentin sialophosphoprotein) This gene encodes a member of the small integrin-binding ligand N-linked glycoprotein (SIBLING) family of proteins. The encoded preproprotein is secreted by odontoblasts and proteolytically processed to generate two principal proteins of the dentin extracellular matrix of the tooth, dentin sialoprotein and dentin phosphoprotein. These two protein products may play distinct but related roles in dentin mineralization. Mutations in this gene are associated with dentinogenesis imperfecta and dentin dysplasia. This gene is present in a gene cluster on chromosome 4. Allelic differences due to repeat polymorphisms have been found for this gene. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 4-87612489-C-T is Benign according to our data. Variant chr4-87612489-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 260357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-87612489-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
BS2
?
High AC in GnomAd4 at 596 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSPP | NM_014208.3 | c.303C>T | p.Asn101= | synonymous_variant | 4/5 | ENST00000651931.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSPP | ENST00000651931.1 | c.303C>T | p.Asn101= | synonymous_variant | 4/5 | NM_014208.3 | P1 | ||
ENST00000506480.5 | n.323-43956G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00392 AC: 594AN: 151692Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00115 AC: 287AN: 249008Hom.: 1 AF XY: 0.000896 AC XY: 121AN XY: 135086
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GnomAD4 exome AF: 0.000704 AC: 1029AN: 1461722Hom.: 4 Cov.: 84 AF XY: 0.000668 AC XY: 486AN XY: 727142
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GnomAD4 genome ? AF: 0.00393 AC: 596AN: 151810Hom.: 4 Cov.: 32 AF XY: 0.00392 AC XY: 291AN XY: 74190
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 29, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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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