rs12435382

chr14-72793669-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001280542.3(DPF3):c.33-21776C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,230 control chromosomes in the GnomAD database, including 1,589 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 0.14 (1589 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

DPF3 (HGNC:17427): (double PHD fingers 3) This gene encodes a member of the D4 protein family. The encoded protein is a transcription regulator that binds acetylated histones and is a component of the BAF chromatin remodeling complex. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPF3	NM_001280542.3	c.33-21776C>T		intron_variant		ENST00000556509.6
DPF3	NM_001280543.2	c.63-21776C>T		intron_variant
DPF3	NM_001280544.2	c.198-21776C>T		intron_variant
DPF3	NM_012074.5	c.33-21776C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPF3	ENST00000556509.6	c.33-21776C>T		intron_variant		1	NM_001280542.3	P1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20896 AN: 152112 Hom.: 1588 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.137 AC: 20904 AN: 152230 Hom.: 1589 Cov.: 32 AF XY: 0.134 AC XY: 9991 AN XY: 74452

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0647

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.176

Alfa AF: 0.167 Hom.: 4510

Bravo AF: 0.143

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.5
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12435382; hg19: chr14-73260377; COSMIC: COSV63503457;