14-72876869-C-T

Position:

• chr14-72876869-C-T

Variant summary

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

The NM_001280542.3(DPF3):​c.32+17188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,216 control chromosomes in the GnomAD database, including 5,027 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 0.22 (5027 hom., cov: 33)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.32+17188G>A		intron_variant		ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.197+15278G>A		intron_variant			NP_001267473.1
DPF3	NM_001280543.2	c.62+2935G>A		intron_variant			NP_001267472.1
DPF3	NM_012074.5	c.32+17188G>A		intron_variant			NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.32+17188G>A		intron_variant		1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33916 AN: 152096 Hom.: 5024 Cov.: 33

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.223 AC: 33922 AN: 152216 Hom.: 5027 Cov.: 33 AF XY: 0.226 AC XY: 16853 AN XY: 74420

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0557

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.201

Alfa AF: 0.281 Hom.: 8421

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.66

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: rs11626844; hg19: chr14-73343577;