chr1-168696736-T-C

Variant names:

• chr1-168696736-T-C
• rs524705
• NM_001937.5:c.540-121A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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)

ENSG00000307075 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.540-121A>G		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.540-121A>G		intron	N/A	ENSP00000356791.3	Q07507
	DPT	ENST00000953565.1		c.591-121A>G		intron	N/A	ENSP00000623624.1
	DPT	ENST00000886480.1		c.432-121A>G		intron	N/A	ENSP00000556539.1

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

African (AFR) AF: 0.806 AC: 13474 AN: 16720

American (AMR) AF: 0.587 AC: 13569 AN: 23134

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 7434 AN: 16338

East Asian (EAS) AF: 0.550 AC: 18100 AN: 32926

South Asian (SAS) AF: 0.630 AC: 33895 AN: 53826

European-Finnish (FIN) AF: 0.528 AC: 21227 AN: 40208

Middle Eastern (MID) AF: 0.579 AC: 2112 AN: 3650

European-Non Finnish (NFE) AF: 0.541 AC: 248295 AN: 458590

Other (OTH) AF: 0.576 AC: 19567 AN: 33982

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

African (AFR) AF: 0.803 AC: 33283 AN: 41438

American (AMR) AF: 0.581 AC: 8890 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1537 AN: 3462

East Asian (EAS) AF: 0.552 AC: 2837 AN: 5136

South Asian (SAS) AF: 0.618 AC: 2971 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5735 AN: 10528

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36273 AN: 67946

Other (OTH) AF: 0.605 AC: 1281 AN: 2116

Alfa AF: 0.560 Hom.: 92556

Bravo AF: 0.626

Asia WGS AF: 0.597 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.43
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs524705; hg19: chr1-168665974; COSMIC: COSV63190735;