rs12435412

chr14-72793767-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.33-21874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,184 control chromosomes in the GnomAD database, including 1,716 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 (1716 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

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=-0.91).
• 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.33-21874C>T		intron_variant		ENST00000556509.6
DPF3	NM_001280543.2	c.63-21874C>T		intron_variant
DPF3	NM_001280544.2	c.198-21874C>T		intron_variant
DPF3	NM_012074.5	c.33-21874C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPF3	ENST00000556509.6	c.33-21874C>T		intron_variant		1	NM_001280542.3	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21991 AN: 152066 Hom.: 1715 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.145 AC: 22000 AN: 152184 Hom.: 1716 Cov.: 32 AF XY: 0.141 AC XY: 10494 AN XY: 74406

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.184

Alfa AF: 0.157 Hom.: 1022

Bravo AF: 0.152

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.33
Dann	Benign	0.48

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: rs12435412; hg19: chr14-73260475;