rs2536143

Variant names:

• chr14-72718325-A-T
• rs2536143
• NM_001280542.3:c.526-3824T>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.526-3824T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,106 control chromosomes in the GnomAD database, including 33,005 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 0.66 (33005 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.526-3824T>A		intron_variant	Intron 5 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.691-3824T>A		intron_variant	Intron 5 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.556-3824T>A		intron_variant	Intron 6 of 10		NP_001267472.1
DPF3	NM_012074.5	c.526-3824T>A		intron_variant	Intron 5 of 9		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.526-3824T>A		intron_variant	Intron 5 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99619 AN: 151988 Hom.: 32990 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.655 AC: 99679 AN: 152106 Hom.: 33005 Cov.: 32 AF XY: 0.660 AC XY: 49093 AN XY: 74344

African (AFR) AF: 0.720 AC: 29859 AN: 41494

American (AMR) AF: 0.674 AC: 10310 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2781 AN: 5158

South Asian (SAS) AF: 0.668 AC: 3217 AN: 4814

European-Finnish (FIN) AF: 0.666 AC: 7058 AN: 10592

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41839 AN: 67968

Other (OTH) AF: 0.690 AC: 1459 AN: 2114

Alfa AF: 0.630 Hom.: 3787

Bravo AF: 0.655

Asia WGS AF: 0.601 AC: 2093 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	0.72
DANN	Benign	0.65
PhyloP100		-0.36
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: rs2536143; hg19: chr14-73185033;