11-103736010-G-A

Variant names:

• chr11-103736010-G-A
• rs17101477
• ENST00000533459.1:n.128-31112C>T

Variant summary

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

The ENST00000533459.1(PDGFDDN):​n.128-31112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 152,260 control chromosomes in the GnomAD database, including 423 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 0.052 (423 hom., cov: 32)
• Consequence: PDGFDDN ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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.128-31112C>T		intron_variant	Intron 2 of 4	4
PDGFDDN	ENST00000812819.1	n.267-55668C>T		intron_variant	Intron 1 of 2
PDGFDDN	ENST00000812820.1	n.149-55668C>T		intron_variant	Intron 1 of 3
PDGFDDN	ENST00000812821.1	n.154-55668C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7956 AN: 152144 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.00998

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0523 AC: 7970 AN: 152260 Hom.: 423 Cov.: 32 AF XY: 0.0521 AC XY: 3881 AN XY: 74438

African (AFR) AF: 0.123 AC: 5092 AN: 41524

American (AMR) AF: 0.0314 AC: 480 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.169 AC: 872 AN: 5166

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4830

European-Finnish (FIN) AF: 0.00998 AC: 106 AN: 10622

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0149 AC: 1017 AN: 68032

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0265 Hom.: 223

Bravo AF: 0.0576

Asia WGS AF: 0.101 AC: 349 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	0.97
DANN	Benign	0.74
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs17101477; hg19: chr11-103606738;