rs1483274

Variant names:

• chr11-103728869-G-A
• rs1483274
• ENST00000533459.1:n.128-23971C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-103728869-G-A
• chr11-103728869-G-C

Variant summary

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

The ENST00000533459.1(PDGFDDN):​n.128-23971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,200 control chromosomes in the GnomAD database, including 65,936 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 0.93 (65936 hom., cov: 30)
• Consequence: PDGFDDN ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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

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	ENST00000533459.1	TSL:4	n.128-23971C>T		intron	N/A
	PDGFDDN	ENST00000812819.1		n.267-48527C>T		intron	N/A
	PDGFDDN	ENST00000812820.1		n.149-48527C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141071 AN: 152082 Hom.: 65897 Cov.: 30

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.927 AC: 141164 AN: 152200 Hom.: 65936 Cov.: 30 AF XY: 0.929 AC XY: 69111 AN XY: 74420

African (AFR) AF: 0.810 AC: 33618 AN: 41498

American (AMR) AF: 0.956 AC: 14628 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3427 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4286 AN: 5154

South Asian (SAS) AF: 0.948 AC: 4563 AN: 4814

European-Finnish (FIN) AF: 0.990 AC: 10507 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66971 AN: 68032

Other (OTH) AF: 0.936 AC: 1976 AN: 2112

Alfa AF: 0.948 Hom.: 9604

Bravo AF: 0.919

Asia WGS AF: 0.895 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1483274; hg19: chr11-103599597;