14-72876869-C-T

Variant names:

• chr14-72876869-C-T
• rs11626844
• NM_001280542.3:c.32+17188G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001280542.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPF3	NM_001280542.3	MANE Select	c.32+17188G>A		intron	N/A	NP_001267471.1	Q92784-1
	DPF3	NM_001280544.2		c.197+15278G>A		intron	N/A	NP_001267473.1	F8W7T1
	DPF3	NM_001280543.2		c.62+2935G>A		intron	N/A	NP_001267472.1	Q92784-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPF3	ENST00000556509.6	TSL:1 MANE Select	c.32+17188G>A		intron	N/A	ENSP00000450518.1	Q92784-1
	DPF3	ENST00000381216.8	TSL:1	n.32+17188G>A		intron	N/A	ENSP00000370614.4	Q92784-2
	DPF3	ENST00000366353.8	TSL:2	n.197+15278G>A		intron	N/A	ENSP00000381791.3	F8W7T1

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

African (AFR) AF: 0.0545 AC: 2266 AN: 41558

American (AMR) AF: 0.194 AC: 2963 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3466

East Asian (EAS) AF: 0.0557 AC: 289 AN: 5192

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4828

European-Finnish (FIN) AF: 0.409 AC: 4326 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21521 AN: 67984

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.273 Hom.: 10250

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.66
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11626844; hg19: chr14-73343577;