chr11-103737242-G-A

Variant names:

• chr11-103737242-G-A
• rs10895516
• ENST00000533459.1:n.128-32344C>T

Variant summary

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

The ENST00000533459.1(PDGFDDN):​n.128-32344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 152,166 control chromosomes in the GnomAD database, including 134 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 0.027 (134 hom., cov: 32)
• Consequence: PDGFDDN ENST00000533459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• 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 (EAS) allele frequency at 95% confidence interval = 0.159 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFDDN	ENST00000533459.1	TSL:4	n.128-32344C>T		intron	N/A
	PDGFDDN	ENST00000812819.1		n.267-56900C>T		intron	N/A
	PDGFDDN	ENST00000812820.1		n.149-56900C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4139 AN: 152048 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.00972

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0272 AC: 4140 AN: 152166 Hom.: 134 Cov.: 32 AF XY: 0.0280 AC XY: 2084 AN XY: 74360

African (AFR) AF: 0.0372 AC: 1544 AN: 41522

American (AMR) AF: 0.0181 AC: 277 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.168 AC: 868 AN: 5162

South Asian (SAS) AF: 0.0505 AC: 243 AN: 4810

European-Finnish (FIN) AF: 0.00972 AC: 103 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 993 AN: 68018

Other (OTH) AF: 0.0241 AC: 51 AN: 2114

Alfa AF: 0.0182 Hom.: 82

Bravo AF: 0.0280

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.50
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10895516; hg19: chr11-103607970;