11-103668768-G-T

Variant names:

• chr11-103668768-G-T
• rs2034557
• ENST00000812819.1:n.375+11466C>A

Variant summary

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

The ENST00000812819.1(PDGFDDN):​n.375+11466C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,044 control chromosomes in the GnomAD database, including 41,468 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 0.73 (41468 hom., cov: 31)
• Consequence: PDGFDDN ENST00000812819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812819.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFDDN	ENST00000812819.1		n.375+11466C>A		intron	N/A
	PDGFDDN	ENST00000812820.1		n.257+11466C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111009 AN: 151926 Hom.: 41425 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.731 AC: 111107 AN: 152044 Hom.: 41468 Cov.: 31 AF XY: 0.729 AC XY: 54144 AN XY: 74322

African (AFR) AF: 0.599 AC: 24843 AN: 41462

American (AMR) AF: 0.716 AC: 10915 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2525 AN: 3466

East Asian (EAS) AF: 0.609 AC: 3133 AN: 5148

South Asian (SAS) AF: 0.659 AC: 3172 AN: 4812

European-Finnish (FIN) AF: 0.860 AC: 9119 AN: 10598

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.809 AC: 54994 AN: 67990

Other (OTH) AF: 0.709 AC: 1498 AN: 2114

Alfa AF: 0.774 Hom.: 5988

Bravo AF: 0.715

Asia WGS AF: 0.658 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.72
PhyloP100		0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2034557;

hg19: chr11-103539496;