rs1106631

Variant names:

• chr14-72787181-C-T
• rs1106631
• NM_001280542.3:c.33-15288G>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.33-15288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,310 control chromosomes in the GnomAD database, including 770 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 (770 hom., cov: 33)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.33-15288G>A		intron_variant	Intron 1 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.198-15288G>A		intron_variant	Intron 1 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.63-15288G>A		intron_variant	Intron 2 of 10		NP_001267472.1
DPF3	NM_012074.5	c.33-15288G>A		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.33-15288G>A		intron_variant	Intron 1 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12444 AN: 152192 Hom.: 768 Cov.: 33

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0817 AC: 12450 AN: 152310 Hom.: 770 Cov.: 33 AF XY: 0.0828 AC XY: 6164 AN XY: 74478

African (AFR) AF: 0.0217 AC: 901 AN: 41568

American (AMR) AF: 0.177 AC: 2701 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3466

East Asian (EAS) AF: 0.0220 AC: 114 AN: 5192

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4826

European-Finnish (FIN) AF: 0.0623 AC: 662 AN: 10624

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

European-Non Finnish (NFE) AF: 0.0984 AC: 6690 AN: 68022

Other (OTH) AF: 0.0728 AC: 154 AN: 2116

Alfa AF: 0.0913 Hom.: 101

Bravo AF: 0.0839

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.54
PhyloP100		0.12
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: rs1106631; hg19: chr14-73253889;