rs10129954

Variant names:

• chr14-72683993-C-T
• rs10129954
• NM_001280542.3:c.742+9083G>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.742+9083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,914 control chromosomes in the GnomAD database, including 20,014 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 0.50 (20014 hom., cov: 31)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.92 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.742+9083G>A		intron	N/A	NP_001267471.1	Q92784-1
	DPF3	NM_001280544.2		c.907+9083G>A		intron	N/A	NP_001267473.1	F8W7T1
	DPF3	NM_001280543.2		c.772+9083G>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.742+9083G>A		intron	N/A	ENSP00000450518.1	Q92784-1
	DPF3	ENST00000381216.8	TSL:1	n.742+9083G>A		intron	N/A	ENSP00000370614.4	Q92784-2
	DPF3	ENST00000366353.8	TSL:2	n.907+9083G>A		intron	N/A	ENSP00000381791.3	F8W7T1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75682 AN: 151796 Hom.: 19988 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.499 AC: 75750 AN: 151914 Hom.: 20014 Cov.: 31 AF XY: 0.512 AC XY: 38016 AN XY: 74260

African (AFR) AF: 0.531 AC: 21955 AN: 41384

American (AMR) AF: 0.608 AC: 9274 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3466

East Asian (EAS) AF: 0.942 AC: 4870 AN: 5170

South Asian (SAS) AF: 0.703 AC: 3381 AN: 4808

European-Finnish (FIN) AF: 0.449 AC: 4731 AN: 10528

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28176 AN: 67976

Other (OTH) AF: 0.527 AC: 1114 AN: 2112

Alfa AF: 0.463 Hom.: 2890

Bravo AF: 0.513

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.22
PhyloP100		0.91
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: rs10129954; hg19: chr14-73150701;