chr14-72810446-G-C

Variant names:

• chr14-72810446-G-C
• rs1990440
• NM_001280542.3:c.33-38553C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001280542.3(DPF3):​c.33-38553C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,226 control chromosomes in the GnomAD database, including 790 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 0.082 (790 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.33-38553C>G		intron_variant	Intron 1 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.198-38553C>G		intron_variant	Intron 1 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.63-38553C>G		intron_variant	Intron 2 of 10		NP_001267472.1
DPF3	NM_012074.5	c.33-38553C>G		intron_variant	Intron 1 of 9		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.33-38553C>G		intron_variant	Intron 1 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12485 AN: 152108 Hom.: 788 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0821 AC: 12492 AN: 152226 Hom.: 790 Cov.: 32 AF XY: 0.0830 AC XY: 6180 AN XY: 74444

African (AFR) AF: 0.0208 AC: 862 AN: 41530

American (AMR) AF: 0.181 AC: 2767 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5178

South Asian (SAS) AF: 0.194 AC: 937 AN: 4820

European-Finnish (FIN) AF: 0.0649 AC: 689 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0999 AC: 6791 AN: 68002

Other (OTH) AF: 0.0749 AC: 158 AN: 2110

Alfa AF: 0.0493 Hom.: 53

Bravo AF: 0.0842

Asia WGS AF: 0.120 AC: 419 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	0.78
DANN	Benign	0.57
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1990440; hg19: chr14-73277154;