11-103866729-T-G

Variant names:

• chr11-103866729-T-G
• rs721346
• ENST00000533459.1:n.127+27146A>C

Variant summary

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

The ENST00000533459.1(PDGFDDN):​n.127+27146A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,254 control chromosomes in the GnomAD database, including 1,392 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 (1392 hom., cov: 32)
• Consequence: PDGFDDN ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFDDN	ENST00000533459.1	TSL:4	n.127+27146A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18235 AN: 152136 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.120 AC: 18233 AN: 152254 Hom.: 1392 Cov.: 32 AF XY: 0.124 AC XY: 9255 AN XY: 74430

African (AFR) AF: 0.0662 AC: 2751 AN: 41562

American (AMR) AF: 0.109 AC: 1669 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1755 AN: 5164

South Asian (SAS) AF: 0.255 AC: 1231 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1271 AN: 10604

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8480 AN: 68016

Other (OTH) AF: 0.141 AC: 298 AN: 2114

Alfa AF: 0.122 Hom.: 1499

Bravo AF: 0.113

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.2
DANN	Benign	0.89
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs721346; hg19: chr11-103737457;