14-72693117-T-C

Position:

• chr14-72693117-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001280542.3(DPF3):​c.701A>G​(p.Glu234Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: DPF3 NM_001280542.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.86

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]

DPF3 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18558097).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.701A>G	p.Glu234Gly	missense_variant	7/11	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.866A>G	p.Glu289Gly	missense_variant	7/10		NP_001267473.1
DPF3	NM_001280543.2	c.731A>G	p.Glu244Gly	missense_variant	8/11		NP_001267472.1
DPF3	NM_012074.5	c.701A>G	p.Glu234Gly	missense_variant	7/10		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.701A>G	p.Glu234Gly	missense_variant	7/11	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 04, 2024

The c.701A>G (p.E234G) alteration is located in exon 7 (coding exon 7) of the DPF3 gene. This alteration results from a A to G substitution at nucleotide position 701, causing the glutamic acid (E) at amino acid position 234 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	T;T;.;.;.
Eigen	Benign	-0.060
Eigen_PC	Benign	0.10
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.88	D;D;D;D;.
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.19	T;T;T;T;T
MetaSVM	Uncertain	0.11	D
MutationAssessor	Benign	1.6	L;.;L;.;.
PrimateAI	Uncertain	0.49	T
PROVEAN	Uncertain	-2.9	D;.;D;.;D
REVEL	Uncertain	0.34
Sift	Benign	0.092	T;.;T;.;T
Sift4G	Benign	0.17	T;T;T;T;T
Polyphen		0.039	B;.;B;.;.
Vest4		0.33
MutPred		0.16		Loss of stability (P = 0.085);.;Loss of stability (P = 0.085);.;.;
MVP		0.36
MPC		0.54
ClinPred		0.82	D
GERP RS		5.4
Varity_R		0.19
gMVP		0.38

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-73159825;