rs1818106

Variant names:

• chr11-104042648-C-A
• rs1818106
• NM_025208.5:c.125-42393G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-104042648-C-A
• chr11-104042648-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025208.5(PDGFD):​c.125-42393G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,008 control chromosomes in the GnomAD database, including 15,463 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 0.44 (15463 hom., cov: 32)
• Consequence: PDGFD NM_025208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 4 publications found

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]

PDGFD Gene-Disease associations (from GenCC):

• pulmonary arterial hypertension

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000300441 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFD	NM_025208.5	c.125-42393G>T		intron_variant	Intron 1 of 6	ENST00000393158.7	NP_079484.1
PDGFD	NM_033135.4	c.125-42411G>T		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.125-42393G>T		intron_variant	Intron 1 of 6	1	NM_025208.5	ENSP00000376865.2
PDGFD	ENST00000302251.9	c.125-42411G>T		intron_variant	Intron 1 of 6	1		ENSP00000302193.5
ENSG00000300441	ENST00000771685.1	n.182-41364C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66378 AN: 151890 Hom.: 15445 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.437 AC: 66421 AN: 152008 Hom.: 15463 Cov.: 32 AF XY: 0.440 AC XY: 32727 AN XY: 74302

African (AFR) AF: 0.268 AC: 11135 AN: 41480

American (AMR) AF: 0.563 AC: 8596 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2218 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4812

European-Finnish (FIN) AF: 0.545 AC: 5735 AN: 10532

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33695 AN: 67958

Other (OTH) AF: 0.432 AC: 914 AN: 2114

Alfa AF: 0.468 Hom.: 28684

Bravo AF: 0.432

Asia WGS AF: 0.450 AC: 1563 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	7.9
DANN	Benign	0.62
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1818106; hg19: chr11-103913376;