rs10129954

Positions:

• chr14-72683993-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556509.6(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 ENST00000556509.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.742+9083G>A		intron_variant		ENST00000556509.6	NP_001267471.1
DPF3	NM_001280543.2	c.772+9083G>A		intron_variant			NP_001267472.1
DPF3	NM_001280544.2	c.907+9083G>A		intron_variant			NP_001267473.1
DPF3	NM_012074.5	c.742+9083G>A		intron_variant			NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.742+9083G>A		intron_variant		1	NM_001280542.3	ENSP00000450518	P1

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.527

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.22

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: rs10129954; hg19: chr14-73150701;