4-87610715-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014208.3(DSPP):c.-28-166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,972 control chromosomes in the GnomAD database, including 6,130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (6130 hom., cov: 32)
• Consequence: DSPP NM_014208.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.370

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-87610715-C-T is Benign according to our data. Variant chr4-87610715-C-T is described in ClinVar as [Benign]. Clinvar id is 1250207.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSPP	NM_014208.3	c.-28-166C>T		intron_variant		ENST00000651931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSPP	ENST00000651931.1	c.-28-166C>T		intron_variant			NM_014208.3	P1
	ENST00000506480.5	n.323-42182G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40520 AN: 151854 Hom.: 6120 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.267 AC: 40548 AN: 151972 Hom.: 6130 Cov.: 32 AF XY: 0.266 AC XY: 19733 AN XY: 74284

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.283

Alfa AF: 0.284 Hom.: 1047

Bravo AF: 0.259

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.28
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs2736980; hg19: chr4-88531867; COSMIC: COSV56817927; COSMIC: COSV56817927;