rs8010957

chr14-72846718-A-Gchr14-72846718-A-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+47339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.974 in 152,072 control chromosomes in the GnomAD database, including 72,144 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 0.97 (72144 hom., cov: 29)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPF3	NM_001280542.3	c.32+47339T>C		intron_variant		ENST00000556509.6
DPF3	NM_001280543.2	c.62+33086T>C		intron_variant
DPF3	NM_001280544.2	c.197+45429T>C		intron_variant
DPF3	NM_012074.5	c.32+47339T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPF3	ENST00000556509.6	c.32+47339T>C		intron_variant		1	NM_001280542.3	P1

Frequencies

GnomAD3 genomes AF: 0.974 AC: 147960 AN: 151954 Hom.: 72081 Cov.: 29

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.974 AC: 148082 AN: 152072 Hom.: 72144 Cov.: 29 AF XY: 0.973 AC XY: 72303 AN XY: 74312

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.991

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.970

Alfa AF: 0.967 Hom.: 3858

Bravo AF: 0.976

Asia WGS AF: 0.994 AC: 3455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.14
Dann	Benign	0.29

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: rs8010957; hg19: chr14-73313426;