rs524705

Positions:

• chr1-168696736-T-C
• chr1-168696736-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001937.5(DPT):​c.540-121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 831,300 control chromosomes in the GnomAD database, including 137,053 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (29837 hom., cov: 30)
  • Exomes 𝑓: 0.56 (107216 hom.)
• Consequence: DPT NM_001937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

Genes affected

DPT (HGNC:3011): (dermatopontin) Dermatopontin is an extracellular matrix protein with possible functions in cell-matrix interactions and matrix assembly. The protein is found in various tissues and many of its tyrosine residues are sulphated. Dermatopontin is postulated to modify the behavior of TGF-beta through interaction with decorin. [provided by RefSeq, Jul 2008]

ENSG00000285622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPT	NM_001937.5	c.540-121A>G		intron_variant		ENST00000367817.4	NP_001928.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPT	ENST00000367817.4	c.540-121A>G		intron_variant		1	NM_001937.5	ENSP00000356791.3
ENSG00000285622	ENST00000650631.1	n.940-121A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93180 AN: 151806 Hom.: 29787 Cov.: 30

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.605

GnomAD4 exome AF: 0.556 AC: 377673 AN: 679374 Hom.: 107216 AF XY: 0.557 AC XY: 197252 AN XY: 354080

Gnomad4 AFR exome AF: 0.806

Gnomad4 AMR exome AF: 0.587

Gnomad4 ASJ exome AF: 0.455

Gnomad4 EAS exome AF: 0.550

Gnomad4 SAS exome AF: 0.630

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.541

Gnomad4 OTH exome AF: 0.576

GnomAD4 genome AF: 0.614 AC: 93288 AN: 151926 Hom.: 29837 Cov.: 30 AF XY: 0.612 AC XY: 45464 AN XY: 74232

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.605

Alfa AF: 0.547 Hom.: 38849

Bravo AF: 0.626

Asia WGS AF: 0.597 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs524705; hg19: chr1-168665974; COSMIC: COSV63190735;