11-103987393-C-T

Variant summary

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

The NM_025208.5(PDGFD):c.510+8672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,940 control chromosomes in the GnomAD database, including 6,387 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 0.27 (6387 hom., cov: 31)
• Consequence: PDGFD NM_025208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

PDGFD (HGNC:30620): (platelet derived growth factor D) The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFD	NM_025208.5	c.510+8672G>A		intron_variant		ENST00000393158.7
PDGFD	NM_033135.4	c.492+8672G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFD	ENST00000393158.7	c.510+8672G>A		intron_variant		1	NM_025208.5	P1
PDGFD	ENST00000302251.9	c.492+8672G>A		intron_variant		1
PDGFD	ENST00000529268.1	c.579+8672G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41168 AN: 151822 Hom.: 6376 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.271 AC: 41196 AN: 151940 Hom.: 6387 Cov.: 31 AF XY: 0.277 AC XY: 20564 AN XY: 74242

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.293

Alfa AF: 0.281 Hom.: 8452

Bravo AF: 0.273

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.27
Dann	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872902; hg19: chr11-103858121;