Variant 4-87611030-AGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014208.3(DSPP):c.51+97_51+104dupTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0231 in 819,362 control chromosomes in the GnomAD database, including 195 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.038 ( 166 hom., cov: 0)

Exomes 𝑓: 0.020 ( 29 hom. )

Consequence

DSPP
NM_014208.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.257

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]

DSPP links:

ENSG00000249001 (HGNC:58144):

ENSG00000249001 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSPP	NM_014208.3 link	c.51+97_51+104dupTGTGTGTG		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
DSPP	ENST00000651931.1 link	c.51+71_51+72insGTGTGTGT		intron_variant	Intron 2 of 4		NM_014208.3	ENSP00000498766.1		Q9NZW4
ENSG00000249001	ENST00000506480.5 link	n.323-42498_323-42497insACACACAC		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5470

AN:

145512

Hom.:

165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.0112

Gnomad AMR

AF:

0.0189

Gnomad ASJ

AF:

0.0347

Gnomad EAS

AF:

0.0384

Gnomad SAS

AF:

0.0233

Gnomad FIN

AF:

0.0483

Gnomad MID

AF:

0.0422

Gnomad NFE

AF:

0.0157

Gnomad OTH

AF:

0.0325

GnomAD4 exome

AF:

0.0199

AC:

13416

AN:

673752

Hom.:

AF XY:

0.0197

AC XY:

7126

AN XY:

361040

show subpopulations

Gnomad4 AFR exome

AF:

0.0748

Gnomad4 AMR exome

AF:

0.0133

Gnomad4 ASJ exome

AF:

0.0352

Gnomad4 EAS exome

AF:

0.0370

Gnomad4 SAS exome

AF:

0.0169

Gnomad4 FIN exome

AF:

0.0442

Gnomad4 NFE exome

AF:

0.0133

Gnomad4 OTH exome

AF:

0.0229

GnomAD4 genome

AF:

0.0376

AC:

5474

AN:

145610

Hom.:

166

Cov.:

AF XY:

0.0383

AC XY:

2702

AN XY:

70582

show subpopulations

Gnomad4 AFR

AF:

0.0820

Gnomad4 AMR

AF:

0.0189

Gnomad4 ASJ

AF:

0.0347

Gnomad4 EAS

AF:

0.0385

Gnomad4 SAS

AF:

0.0231

Gnomad4 FIN

AF:

0.0483

Gnomad4 NFE

AF:

0.0157

Gnomad4 OTH

AF:

0.0322

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over