Variant 4-87611030-AGT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014208.3(DSPP):c.51+103_51+104delTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 811,470 control chromosomes in the GnomAD database, including 1,756 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1278 hom., cov: 0)

Exomes 𝑓: 0.14 ( 478 hom. )

Consequence

DSPP
NM_014208.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-87611030-AGT-A is Benign according to our data. Variant chr4-87611030-AGT-A is described in ClinVar as [Benign]. Clinvar id is 1281125.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSPP	NM_014208.3 link	c.51+103_51+104delTG		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+72_51+73delGT		intron_variant	Intron 2 of 4		NM_014208.3	ENSP00000498766.1		Q9NZW4
ENSG00000249001	ENST00000506480.5 link	n.323-42499_323-42498delAC		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18041

AN:

145456

Hom.:

1280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0975

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.0878

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.172

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.140

AC:

93366

AN:

665916

Hom.:

478

AF XY:

0.148

AC XY:

52788

AN XY:

356838

show subpopulations

Gnomad4 AFR exome

AF:

0.0997

Gnomad4 AMR exome

AF:

0.0794

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.294

Gnomad4 SAS exome

AF:

0.255

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.124

AC:

18044

AN:

145554

Hom.:

1278

Cov.:

AF XY:

0.128

AC XY:

9048

AN XY:

70550

show subpopulations

Gnomad4 AFR

AF:

0.0975

Gnomad4 AMR

AF:

0.0876

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.296

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.133

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 18, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over