11-103937424-C-T

Variant names:

• chr11-103937424-C-T
• rs10895547
• NM_025208.5:c.772+6028G>A

Variant summary

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

The NM_025208.5(PDGFD):​c.772+6028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,902 control chromosomes in the GnomAD database, including 8,247 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 0.32 (8247 hom., cov: 31)
• Consequence: PDGFD NM_025208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFD	NM_025208.5	c.772+6028G>A		intron_variant	Intron 5 of 6	ENST00000393158.7	NP_079484.1
PDGFD	NM_033135.4	c.754+6028G>A		intron_variant	Intron 5 of 6		NP_149126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFD	ENST00000393158.7	c.772+6028G>A		intron_variant	Intron 5 of 6	1	NM_025208.5	ENSP00000376865.2
PDGFD	ENST00000302251.9	c.754+6028G>A		intron_variant	Intron 5 of 6	1		ENSP00000302193.5

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48878 AN: 151784 Hom.: 8252 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.322 AC: 48886 AN: 151902 Hom.: 8247 Cov.: 31 AF XY: 0.322 AC XY: 23895 AN XY: 74228

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.317

Alfa AF: 0.363 Hom.: 15705

Bravo AF: 0.310

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.33
DANN	Benign	0.35

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: rs10895547; hg19: chr11-103808152;