chr4-156864302-G-A

Variant names:

• chr4-156864302-G-A
• rs6811964
• NM_016205.3:c.119-13886C>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.119-13886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,920 control chromosomes in the GnomAD database, including 1,403 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 (1403 hom., cov: 32)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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 (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFC	NM_016205.3	c.119-13886C>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.119-13886C>T		intron_variant	Intron 1 of 5	1	NM_016205.3	ENSP00000422464.1
PDGFC	ENST00000274071.6	n.119-2813C>T		intron_variant	Intron 1 of 6	1		ENSP00000274071.2
PDGFC	ENST00000422544.2	c.119-13886C>T		intron_variant	Intron 1 of 5	5		ENSP00000410048.2
PDGFC	ENST00000512711.1	n.68-2813C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18331 AN: 151804 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0584

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.121 AC: 18341 AN: 151920 Hom.: 1403 Cov.: 32 AF XY: 0.118 AC XY: 8734 AN XY: 74230

African (AFR) AF: 0.217 AC: 8973 AN: 41368

American (AMR) AF: 0.0791 AC: 1206 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3466

East Asian (EAS) AF: 0.0767 AC: 397 AN: 5174

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4824

European-Finnish (FIN) AF: 0.0584 AC: 617 AN: 10560

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0852 AC: 5788 AN: 67968

Other (OTH) AF: 0.126 AC: 265 AN: 2108

Alfa AF: 0.101 Hom.: 1523

Bravo AF: 0.129

Asia WGS AF: 0.0760 AC: 266 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.35
PhyloP100		0.37
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

Publications

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Other links and lift over

dbSNP: rs6811964; hg19: chr4-157785454;