rs1123135

Variant names:

• chr14-72831859-G-A
• rs1123135
• NM_001280542.3:c.33-59966C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001280542.3(DPF3):​c.33-59966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,238 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 4 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 (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.33-59966C>T		intron_variant	Intron 1 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.198-59966C>T		intron_variant	Intron 1 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.62+47945C>T		intron_variant	Intron 2 of 10		NP_001267472.1
DPF3	NM_012074.5	c.33-59966C>T		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.33-59966C>T		intron_variant	Intron 1 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19066 AN: 152120 Hom.: 1419 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.125 AC: 19101 AN: 152238 Hom.: 1423 Cov.: 33 AF XY: 0.124 AC XY: 9211 AN XY: 74440

African (AFR) AF: 0.180 AC: 7468 AN: 41530

American (AMR) AF: 0.186 AC: 2842 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3470

East Asian (EAS) AF: 0.0202 AC: 105 AN: 5190

South Asian (SAS) AF: 0.178 AC: 859 AN: 4824

European-Finnish (FIN) AF: 0.0734 AC: 779 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0979 AC: 6660 AN: 68008

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.109 Hom.: 673

Bravo AF: 0.133

Asia WGS AF: 0.122 AC: 426 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	0.77
DANN	Benign	0.32
PhyloP100		-0.61
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: rs1123135; hg19: chr14-73298567;