chr1-168720702-C-T

Variant names:

• chr1-168720702-C-T
• rs545833
• NM_001937.5:c.306-6356G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001937.5(DPT):​c.306-6356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,998 control chromosomes in the GnomAD database, including 7,134 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 0.30 (7134 hom., cov: 32)
• Consequence: DPT NM_001937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 17 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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.306-6356G>A		intron	N/A	NP_001928.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPT	ENST00000367817.4	TSL:1 MANE Select	c.306-6356G>A		intron	N/A	ENSP00000356791.3	Q07507
	DPT	ENST00000953565.1		c.306-6356G>A		intron	N/A	ENSP00000623624.1
	DPT	ENST00000886480.1		c.306-6356G>A		intron	N/A	ENSP00000556539.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45241 AN: 151880 Hom.: 7113 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.298 AC: 45309 AN: 151998 Hom.: 7134 Cov.: 32 AF XY: 0.307 AC XY: 22825 AN XY: 74270

African (AFR) AF: 0.287 AC: 11877 AN: 41454

American (AMR) AF: 0.346 AC: 5278 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 844 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2688 AN: 5168

South Asian (SAS) AF: 0.429 AC: 2059 AN: 4804

European-Finnish (FIN) AF: 0.359 AC: 3786 AN: 10548

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17832 AN: 67986

Other (OTH) AF: 0.307 AC: 646 AN: 2106

Alfa AF: 0.278 Hom.: 26965

Bravo AF: 0.295

Asia WGS AF: 0.474 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		0.080
Mutation Taster		=100/0	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: rs545833; hg19: chr1-168689940; COSMIC: COSV63190933;