rs2034558

Variant names:

• chr11-103668718-G-A
• rs2034558
• ENST00000812819.1:n.375+11516C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-103668718-G-A
• chr11-103668718-G-T

Variant summary

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

The ENST00000812819.1(PDGFDDN):​n.375+11516C>T 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 152,104 control chromosomes in the GnomAD database, including 41,475 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 (41475 hom., cov: 32)
• Consequence: PDGFDDN ENST00000812819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• 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=-0.91).
• 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+11516C>T		intron	N/A
	PDGFDDN	ENST00000812820.1		n.257+11516C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111053 AN: 151986 Hom.: 41432 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.715

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: 111151 AN: 152104 Hom.: 41475 Cov.: 32 AF XY: 0.729 AC XY: 54161 AN XY: 74332

African (AFR) AF: 0.599 AC: 24856 AN: 41482

American (AMR) AF: 0.716 AC: 10926 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2527 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3139 AN: 5154

South Asian (SAS) AF: 0.659 AC: 3180 AN: 4822

European-Finnish (FIN) AF: 0.861 AC: 9111 AN: 10584

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55006 AN: 68010

Other (OTH) AF: 0.708 AC: 1496 AN: 2112

Alfa AF: 0.774 Hom.: 5988

Bravo AF: 0.715

Asia WGS AF: 0.657 AC: 2289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.69
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: rs2034558;

hg19: chr11-103539446;