rs4554859

Variant names:

• chr11-103659638-G-T
• rs4554859
• ENST00000812819.1:n.376-20553C>A

Variant summary

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

The ENST00000812819.1(PDGFDDN):​n.376-20553C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,906 control chromosomes in the GnomAD database, including 19,696 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 0.48 (19696 hom., cov: 31)
• Consequence: PDGFDDN ENST00000812819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 7 publications found

Genes affected

PDGFDDN (HGNC:56909):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFDDN	ENST00000812819.1	n.376-20553C>A		intron_variant	Intron 2 of 2
PDGFDDN	ENST00000812820.1	n.258-8543C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73510 AN: 151788 Hom.: 19688 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.484 AC: 73536 AN: 151906 Hom.: 19696 Cov.: 31 AF XY: 0.484 AC XY: 35959 AN XY: 74246

African (AFR) AF: 0.245 AC: 10166 AN: 41438

American (AMR) AF: 0.532 AC: 8106 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2493 AN: 5158

South Asian (SAS) AF: 0.467 AC: 2244 AN: 4806

European-Finnish (FIN) AF: 0.632 AC: 6667 AN: 10542

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40280 AN: 67932

Other (OTH) AF: 0.488 AC: 1031 AN: 2112

Alfa AF: 0.447 Hom.: 6457

Bravo AF: 0.466

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4554859; hg19: chr11-103530366;