11-103718366-C-T

Variant names:

• chr11-103718366-C-T
• rs1917445
• ENST00000533459.1:n.128-13468G>A

Variant summary

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

The ENST00000533459.1(PDGFDDN):​n.128-13468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,992 control chromosomes in the GnomAD database, including 17,214 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 0.45 (17214 hom., cov: 32)
• Consequence: PDGFDDN ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 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	ENST00000533459.1	n.128-13468G>A		intron_variant	Intron 2 of 4	4
PDGFDDN	ENST00000812819.1	n.267-38024G>A		intron_variant	Intron 1 of 2
PDGFDDN	ENST00000812820.1	n.149-38024G>A		intron_variant	Intron 1 of 3
PDGFDDN	ENST00000812821.1	n.154-38024G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68327 AN: 151874 Hom.: 17208 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.450 AC: 68348 AN: 151992 Hom.: 17214 Cov.: 32 AF XY: 0.455 AC XY: 33766 AN XY: 74282

African (AFR) AF: 0.211 AC: 8760 AN: 41484

American (AMR) AF: 0.557 AC: 8515 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5170

South Asian (SAS) AF: 0.479 AC: 2309 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6410 AN: 10528

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36375 AN: 67932

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.402 Hom.: 3695

Bravo AF: 0.438

Asia WGS AF: 0.493 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.32
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1917445; hg19: chr11-103589094;