1-168728935-C-T

Variant names:

• chr1-168728935-C-T
• rs1052591
• NM_001937.5:c.240G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001937.5(DPT):​c.240G>A​(p.Thr80Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,613,916 control chromosomes in the GnomAD database, including 204,390 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 0.43 (15462 hom., cov: 32)
  • Exomes 𝑓: 0.50 (188928 hom.)
• Consequence: DPT NM_001937.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.42
• Publications: 18 publications found

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]

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP7: Synonymous conserved (PhyloP=-5.42 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001937.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPT	NM_001937.5	MANE Select	c.240G>A	p.Thr80Thr	synonymous	Exon 1 of 4	NP_001928.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPT	ENST00000367817.4	TSL:1 MANE Select	c.240G>A	p.Thr80Thr	synonymous	Exon 1 of 4	ENSP00000356791.3
	DPT	ENST00000953565.1		c.240G>A	p.Thr80Thr	synonymous	Exon 1 of 5	ENSP00000623624.1
	DPT	ENST00000886480.1		c.240G>A	p.Thr80Thr	synonymous	Exon 1 of 3	ENSP00000556539.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65993 AN: 151920 Hom.: 15465 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.444

GnomAD2 exomes AF: 0.427 AC: 107125 AN: 250962 AF XY: 0.435

Gnomad AFR exome AF: 0.308

Gnomad AMR exome AF: 0.263

Gnomad ASJ exome AF: 0.555

Gnomad EAS exome AF: 0.161

Gnomad FIN exome AF: 0.467

Gnomad NFE exome AF: 0.534

Gnomad OTH exome AF: 0.462

GnomAD4 exome AF: 0.499 AC: 730028 AN: 1461878 Hom.: 188928 Cov.: 73 AF XY: 0.497 AC XY: 361119 AN XY: 727240

African (AFR) AF: 0.299 AC: 10027 AN: 33480

American (AMR) AF: 0.274 AC: 12274 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 14586 AN: 26136

East Asian (EAS) AF: 0.178 AC: 7062 AN: 39700

South Asian (SAS) AF: 0.363 AC: 31299 AN: 86258

European-Finnish (FIN) AF: 0.477 AC: 25472 AN: 53420

Middle Eastern (MID) AF: 0.391 AC: 2258 AN: 5768

European-Non Finnish (NFE) AF: 0.539 AC: 598920 AN: 1111996

Other (OTH) AF: 0.466 AC: 28130 AN: 60396

GnomAD4 genome AF: 0.434 AC: 65997 AN: 152038 Hom.: 15462 Cov.: 32 AF XY: 0.426 AC XY: 31637 AN XY: 74342

African (AFR) AF: 0.309 AC: 12803 AN: 41438

American (AMR) AF: 0.366 AC: 5594 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1941 AN: 3468

East Asian (EAS) AF: 0.164 AC: 845 AN: 5168

South Asian (SAS) AF: 0.359 AC: 1735 AN: 4830

European-Finnish (FIN) AF: 0.456 AC: 4825 AN: 10576

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36450 AN: 67960

Other (OTH) AF: 0.443 AC: 936 AN: 2112

Alfa AF: 0.484 Hom.: 53932

Bravo AF: 0.417

Asia WGS AF: 0.265 AC: 922 AN: 3478

EpiCase AF: 0.526

EpiControl AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.11
DANN	Benign	0.81
PhyloP100		-5.4
PromoterAI		-0.014	Neutral
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1052591; hg19: chr1-168698173; COSMIC: COSV63189989;