NM_025208.5:c.124+17443T>C

Variant names:

• chr11-104146361-A-G
• rs10750684
• NM_025208.5:c.124+17443T>C

Variant summary

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

The NM_025208.5(PDGFD):​c.124+17443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,996 control chromosomes in the GnomAD database, including 26,359 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 0.59 (26359 hom., cov: 32)
• Consequence: PDGFD NM_025208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFD	NM_025208.5	c.124+17443T>C		intron_variant	Intron 1 of 6	ENST00000393158.7	NP_079484.1
PDGFD	NM_033135.4	c.124+17443T>C		intron_variant	Intron 1 of 6		NP_149126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFD	ENST00000393158.7	c.124+17443T>C		intron_variant	Intron 1 of 6	1	NM_025208.5	ENSP00000376865.2
PDGFD	ENST00000302251.9	c.124+17443T>C		intron_variant	Intron 1 of 6	1		ENSP00000302193.5

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88844 AN: 151878 Hom.: 26316 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.585 AC: 88935 AN: 151996 Hom.: 26359 Cov.: 32 AF XY: 0.586 AC XY: 43562 AN XY: 74316

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.575

Alfa AF: 0.586 Hom.: 3757

Bravo AF: 0.590

Asia WGS AF: 0.634 AC: 2203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.43

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: rs10750684; hg19: chr11-104017089;