rs36228864
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-T
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTGTG
- chr4-87612011-TTGTGTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTGTGTG
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_014208.3(DSPP):c.52-81_52-64delTGTGTGTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,068,668 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000011 ( 0 hom. )
Consequence
DSPP
NM_014208.3 intron
NM_014208.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.37
Publications
1 publications found
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]
DSPP Gene-Disease associations (from GenCC):
- deafness, autosomal dominant 39, with dentinogenesis imperfecta 1Inheritance: AD, Unknown Classification: DEFINITIVE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- dentinogenesis imperfectaInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- dentinogenesis imperfecta type 2Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
- dentinogenesis imperfecta type 3Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
- dentin dysplasia type IInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- dentin dysplasia type IIInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014208.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DSPP | MANE Select | c.52-93_52-76delTGTGTGTGTGTGTGTGTG | intron | N/A | ENSP00000498766.1 | Q9NZW4 | |||
| DMP1-AS1 | TSL:3 | n.323-43496_323-43479delCACACACACACACACACA | intron | N/A | |||||
| DMP1-AS1 | n.357-43496_357-43479delCACACACACACACACACA | intron | N/A |
Frequencies
GnomAD3 genomes 0.00000667 AC: 1AN: 149980Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
149980
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000109 AC: 1AN: 918688Hom.: 0 AF XY: 0.00000211 AC XY: 1AN XY: 473170 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
918688
Hom.:
AF XY:
AC XY:
1
AN XY:
473170
show subpopulations
African (AFR)
AF:
AC:
0
AN:
21316
American (AMR)
AF:
AC:
0
AN:
36880
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21592
East Asian (EAS)
AF:
AC:
0
AN:
33230
South Asian (SAS)
AF:
AC:
0
AN:
68370
European-Finnish (FIN)
AF:
AC:
0
AN:
48262
Middle Eastern (MID)
AF:
AC:
0
AN:
3190
European-Non Finnish (NFE)
AF:
AC:
1
AN:
644248
Other (OTH)
AF:
AC:
0
AN:
41600
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000667 AC: 1AN: 149980Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 73122 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
149980
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
73122
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
40738
American (AMR)
AF:
AC:
0
AN:
15074
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3450
East Asian (EAS)
AF:
AC:
0
AN:
5050
South Asian (SAS)
AF:
AC:
0
AN:
4730
European-Finnish (FIN)
AF:
AC:
0
AN:
10346
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67334
Other (OTH)
AF:
AC:
0
AN:
2060
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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