rs11728198

Variant names:

• chr4-156904245-G-A
• rs11728198
• NM_016205.3:c.119-53829C>T

Variant summary

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

The NM_016205.3(PDGFC):​c.119-53829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,754 control chromosomes in the GnomAD database, including 27,470 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 0.60 (27470 hom., cov: 31)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 4 publications found

Genes affected

PDGFC (HGNC:8801): (platelet derived growth factor C) 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. This gene product appears to form only homodimers. It differs from the platelet-derived growth factor alpha and beta polypeptides in having an unusual N-terminal domain, the CUB domain. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFC	NM_016205.3	c.119-53829C>T		intron_variant	Intron 1 of 5	ENST00000502773.6	NP_057289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFC	ENST00000502773.6	c.119-53829C>T		intron_variant	Intron 1 of 5	1	NM_016205.3	ENSP00000422464.1
PDGFC	ENST00000274071.6	n.119-42756C>T		intron_variant	Intron 1 of 6	1		ENSP00000274071.2
PDGFC	ENST00000422544.2	c.119-53829C>T		intron_variant	Intron 1 of 5	5		ENSP00000410048.2

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90915 AN: 151636 Hom.: 27439 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.600 AC: 91009 AN: 151754 Hom.: 27470 Cov.: 31 AF XY: 0.601 AC XY: 44571 AN XY: 74142

African (AFR) AF: 0.605 AC: 25049 AN: 41404

American (AMR) AF: 0.650 AC: 9902 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3466

East Asian (EAS) AF: 0.697 AC: 3569 AN: 5124

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4816

European-Finnish (FIN) AF: 0.652 AC: 6888 AN: 10562

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40314 AN: 67828

Other (OTH) AF: 0.599 AC: 1261 AN: 2106

Alfa AF: 0.587 Hom.: 76474

Bravo AF: 0.601

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		0.38
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: rs11728198; hg19: chr4-157825397;