chr1-168714238-C-T

Variant names:

• chr1-168714238-C-T
• rs35449613
• NM_001937.5:c.414G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Moderate BP6_Moderate BP7 BA1

The NM_001937.5(DPT):​c.414G>A​(p.Arg138Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 1,614,010 control chromosomes in the GnomAD database, including 2,943 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.041 (165 hom., cov: 32)
  • Exomes 𝑓: 0.059 (2778 hom.)
• Consequence: DPT NM_001937.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.230
• Publications: 5 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=-0.42).
• BP6: Variant 1-168714238-C-T is Benign according to our data. Variant chr1-168714238-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3273675.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.23 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0626 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.414G>A	p.Arg138Arg	synonymous	Exon 2 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.414G>A	p.Arg138Arg	synonymous	Exon 2 of 4	ENSP00000356791.3	Q07507
	DPT	ENST00000953565.1		c.414G>A	p.Arg138Arg	synonymous	Exon 2 of 5	ENSP00000623624.1
	DPT	ENST00000886480.1		c.414G>A	p.Arg138Arg	synonymous	Exon 2 of 3	ENSP00000556539.1

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6219 AN: 152072 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0430

GnomAD2 exomes AF: 0.0476 AC: 11963 AN: 251260 AF XY: 0.0507

Gnomad AFR exome AF: 0.0113

Gnomad AMR exome AF: 0.0211

Gnomad ASJ exome AF: 0.0387

Gnomad EAS exome AF: 0.000490

Gnomad FIN exome AF: 0.0384

Gnomad NFE exome AF: 0.0641

Gnomad OTH exome AF: 0.0483

GnomAD4 exome AF: 0.0586 AC: 85664 AN: 1461820 Hom.: 2778 Cov.: 31 AF XY: 0.0592 AC XY: 43025 AN XY: 727216

African (AFR) AF: 0.00836 AC: 280 AN: 33478

American (AMR) AF: 0.0219 AC: 979 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 985 AN: 26134

East Asian (EAS) AF: 0.000227 AC: 9 AN: 39698

South Asian (SAS) AF: 0.0730 AC: 6294 AN: 86250

European-Finnish (FIN) AF: 0.0397 AC: 2121 AN: 53414

Middle Eastern (MID) AF: 0.0525 AC: 303 AN: 5768

European-Non Finnish (NFE) AF: 0.0642 AC: 71416 AN: 1111964

Other (OTH) AF: 0.0543 AC: 3277 AN: 60392

GnomAD4 genome AF: 0.0409 AC: 6217 AN: 152190 Hom.: 165 Cov.: 32 AF XY: 0.0400 AC XY: 2974 AN XY: 74400

African (AFR) AF: 0.0110 AC: 456 AN: 41510

American (AMR) AF: 0.0338 AC: 517 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0687 AC: 331 AN: 4820

European-Finnish (FIN) AF: 0.0354 AC: 375 AN: 10598

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4266 AN: 68018

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0299 Hom.: 19

Bravo AF: 0.0385

Asia WGS AF: 0.0260 AC: 91 AN: 3478

EpiCase AF: 0.0631

EpiControl AF: 0.0609

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	2.4
DANN	Benign	0.87
PhyloP100		-0.23
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: rs35449613; hg19: chr1-168683476;