chr14-72760199-G-A

Variant names:

• chr14-72760199-G-A
• rs11561560
• NM_001280542.3:c.194-6828C>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.194-6828C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 152,148 control chromosomes in the GnomAD database, including 574 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 0.070 (574 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.194-6828C>T		intron_variant	Intron 2 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.359-6828C>T		intron_variant	Intron 2 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.224-6828C>T		intron_variant	Intron 3 of 10		NP_001267472.1
DPF3	NM_012074.5	c.194-6828C>T		intron_variant	Intron 2 of 9		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.194-6828C>T		intron_variant	Intron 2 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 10602 AN: 152030 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0480

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0696 AC: 10595 AN: 152148 Hom.: 574 Cov.: 32 AF XY: 0.0761 AC XY: 5658 AN XY: 74380

African (AFR) AF: 0.0402 AC: 1670 AN: 41498

American (AMR) AF: 0.166 AC: 2529 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3470

East Asian (EAS) AF: 0.143 AC: 741 AN: 5182

South Asian (SAS) AF: 0.164 AC: 790 AN: 4812

European-Finnish (FIN) AF: 0.0880 AC: 931 AN: 10580

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0480 AC: 3266 AN: 68010

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0241 Hom.: 11

Bravo AF: 0.0744

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.40
PhyloP100		-0.30
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: rs11561560; hg19: chr14-73226907;