chr11-103990111-T-C

Position:

• chr11-103990111-T-C

Variant summary

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

The NM_025208.5(PDGFD):​c.510+5954A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,162 control chromosomes in the GnomAD database, including 1,381 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 0.12 (1381 hom., cov: 31)
• Consequence: PDGFD NM_025208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFD	NM_025208.5	c.510+5954A>G		intron_variant		ENST00000393158.7
PDGFD	NM_033135.4	c.492+5954A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFD	ENST00000393158.7	c.510+5954A>G		intron_variant		1	NM_025208.5	P1
PDGFD	ENST00000302251.9	c.492+5954A>G		intron_variant		1
PDGFD	ENST00000529268.1	c.579+5954A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18591 AN: 152044 Hom.: 1381 Cov.: 31

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.122 AC: 18591 AN: 152162 Hom.: 1381 Cov.: 31 AF XY: 0.120 AC XY: 8903 AN XY: 74388

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.139

Alfa AF: 0.134 Hom.: 228

Bravo AF: 0.120

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.65

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: rs10895556; hg19: chr11-103860839;