rs7118412

Variant names:

• chr11-103655026-A-G
• rs7118412
• ENST00000812819.1:n.376-15941T>C

Variant summary

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

The ENST00000812819.1(PDGFDDN):​n.376-15941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,998 control chromosomes in the GnomAD database, including 19,174 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 0.47 (19174 hom., cov: 32)
• Consequence: PDGFDDN ENST00000812819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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.376-15941T>C		intron_variant	Intron 2 of 2
PDGFDDN	ENST00000812820.1	n.258-3931T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71560 AN: 151880 Hom.: 19166 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.471 AC: 71583 AN: 151998 Hom.: 19174 Cov.: 32 AF XY: 0.472 AC XY: 35041 AN XY: 74290

African (AFR) AF: 0.205 AC: 8519 AN: 41512

American (AMR) AF: 0.525 AC: 8003 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1867 AN: 3460

East Asian (EAS) AF: 0.485 AC: 2506 AN: 5170

South Asian (SAS) AF: 0.468 AC: 2255 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6587 AN: 10554

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40170 AN: 67912

Other (OTH) AF: 0.478 AC: 1007 AN: 2108

Alfa AF: 0.449 Hom.: 9884

Bravo AF: 0.451

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.79
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7118412; hg19: chr11-103525754;