11-103902439-T-C

Position:

• chr11-103902439-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_947960.3(PDGFDDN):​n.2191+2241A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,000 control chromosomes in the GnomAD database, including 4,622 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 0.24 (4622 hom., cov: 32)
• Consequence: PDGFDDN XR_947960.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

PDGFDDN (HGNC:56909):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDGFDDN	XR_947960.3	n.2191+2241A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36811 AN: 151882 Hom.: 4620 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.242 AC: 36825 AN: 152000 Hom.: 4622 Cov.: 32 AF XY: 0.238 AC XY: 17714 AN XY: 74282

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.208

Alfa AF: 0.233 Hom.: 3777

Bravo AF: 0.242

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754095; hg19: chr11-103773167;