rs7103004

Variant names:

• chr11-103655296-C-T
• rs7103004
• ENST00000812819.1:n.376-16211G>A

Variant summary

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

The ENST00000812819.1(PDGFDDN):​n.376-16211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,876 control chromosomes in the GnomAD database, including 19,726 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 0.49 (19726 hom., cov: 32)
• Consequence: PDGFDDN ENST00000812819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 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 (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.376-16211G>A		intron_variant	Intron 2 of 2
PDGFDDN	ENST00000812820.1	n.258-4201G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73900 AN: 151760 Hom.: 19719 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.487 AC: 73927 AN: 151876 Hom.: 19726 Cov.: 32 AF XY: 0.487 AC XY: 36127 AN XY: 74234

African (AFR) AF: 0.258 AC: 10682 AN: 41414

American (AMR) AF: 0.532 AC: 8112 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3464

East Asian (EAS) AF: 0.485 AC: 2495 AN: 5144

South Asian (SAS) AF: 0.468 AC: 2258 AN: 4822

European-Finnish (FIN) AF: 0.626 AC: 6614 AN: 10568

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40196 AN: 67914

Other (OTH) AF: 0.487 AC: 1025 AN: 2104

Alfa AF: 0.478 Hom.: 10901

Bravo AF: 0.469

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.91
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7103004; hg19: chr11-103526024;