GeneBe

rs33940466

Variant names:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_014208.3(DSPP):​c.51+93_51+104delTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00193 in 821,884 control chromosomes in the GnomAD database, including 10 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0067 ( 10 hom., cov: 0)
Exomes 𝑓: 0.00091 ( 0 hom. )

Consequence

DSPP
NM_014208.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272
Variant links:
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 -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00666 (970/145690) while in subpopulation AFR AF= 0.0227 (885/38992). AF 95% confidence interval is 0.0215. There are 10 homozygotes in gnomad4. There are 463 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 970 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DSPPNM_014208.3 linkc.51+93_51+104delTGTGTGTGTGTG intron_variant Intron 2 of 4 ENST00000651931.1 NP_055023.2 Q9NZW4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DSPPENST00000651931.1 linkc.51+72_51+83delGTGTGTGTGTGT intron_variant Intron 2 of 4 NM_014208.3 ENSP00000498766.1 Q9NZW4
ENSG00000249001ENST00000506480.5 linkn.323-42509_323-42498delACACACACACAC intron_variant Intron 3 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.00668
AC:
972
AN:
145592
Hom.:
10
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0228
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00447
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000443
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000751
Gnomad OTH
AF:
0.00650
GnomAD4 exome
AF:
0.000912
AC:
617
AN:
676194
Hom.:
0
AF XY:
0.000737
AC XY:
267
AN XY:
362450
show subpopulations
Gnomad4 AFR exome
AF:
0.0245
Gnomad4 AMR exome
AF:
0.00178
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000438
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000903
Gnomad4 OTH exome
AF:
0.00192
GnomAD4 genome
AF:
0.00666
AC:
970
AN:
145690
Hom.:
10
Cov.:
0
AF XY:
0.00656
AC XY:
463
AN XY:
70614
show subpopulations
Gnomad4 AFR
AF:
0.0227
Gnomad4 AMR
AF:
0.00446
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000444
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000751
Gnomad4 OTH
AF:
0.00644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs33940466; hg19: chr4-88532182; API