chr4-156972019-C-G

Variant names:

• chr4-156972019-C-G
• rs1002091
• NM_016205.3:c.-1116G>C

Variant summary

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

The NM_016205.3(PDGFC):​c.-1116G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,012 control chromosomes in the GnomAD database, including 28,889 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 0.61 (28889 hom., cov: 34)
• Consequence: PDGFC NM_016205.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016205.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFC	NM_016205.3	MANE Select	c.-1116G>C		upstream_gene	N/A	NP_057289.1
	PDGFC	NR_036641.2		n.-220G>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFC	ENST00000502773.6	TSL:1 MANE Select	c.-1116G>C		upstream_gene	N/A	ENSP00000422464.1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92616 AN: 151898 Hom.: 28880 Cov.: 34

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.610 AC: 92654 AN: 152012 Hom.: 28889 Cov.: 34 AF XY: 0.604 AC XY: 44850 AN XY: 74286

African (AFR) AF: 0.480 AC: 19902 AN: 41498

American (AMR) AF: 0.672 AC: 10266 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3466

East Asian (EAS) AF: 0.498 AC: 2530 AN: 5078

South Asian (SAS) AF: 0.491 AC: 2370 AN: 4826

European-Finnish (FIN) AF: 0.648 AC: 6870 AN: 10600

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46478 AN: 67950

Other (OTH) AF: 0.652 AC: 1375 AN: 2110

Alfa AF: 0.643 Hom.: 3983

Bravo AF: 0.610

Asia WGS AF: 0.520 AC: 1811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.40
PhyloP100		0.27
PromoterAI		-0.0060	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1002091; hg19: chr4-157893171;