Variant chr14-72753312-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001280542.3(DPF3):c.253T>C(p.Leu85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,613,002 control chromosomes in the GnomAD database, including 59,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4130 hom., cov: 32)

Exomes 𝑓: 0.27 ( 55197 hom. )

Consequence

DPF3
NM_001280542.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.81

Variant links:

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]

DPF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 14-72753312-A-G is Benign according to our data. Variant chr14-72753312-A-G is described in ClinVar as [Benign]. Clinvar id is 1238152.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
DPF3	NM_001280542.3 linkuse as main transcript	c.253T>C	p.Leu85=	synonymous_variant	3/11	ENST00000556509.6
DPF3	NM_001280544.2 linkuse as main transcript	c.418T>C	p.Leu140=	synonymous_variant	3/10
DPF3	NM_001280543.2 linkuse as main transcript	c.283T>C	p.Leu95=	synonymous_variant	4/11
DPF3	NM_012074.5 linkuse as main transcript	c.253T>C	p.Leu85=	synonymous_variant	3/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPF3	ENST00000556509.6 linkuse as main transcript	c.253T>C	p.Leu85=	synonymous_variant	3/11	1	NM_001280542.3	P1	Q92784-1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33291

AN:

151992

Hom.:

4124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.252

GnomAD3 exomes

AF:

0.249

AC:

61919

AN:

248236

Hom.:

8231

AF XY:

0.256

AC XY:

34538

AN XY:

134696

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.305

Gnomad EAS exome

AF:

0.284

Gnomad SAS exome

AF:

0.292

Gnomad FIN exome

AF:

0.157

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.262

GnomAD4 exome

AF:

0.271

AC:

396016

AN:

1460892

Hom.:

55197

Cov.:

AF XY:

0.273

AC XY:

198265

AN XY:

726736

show subpopulations

Gnomad4 AFR exome

AF:

0.0981

Gnomad4 AMR exome

AF:

0.212

Gnomad4 ASJ exome

AF:

0.305

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.291

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.284

Gnomad4 OTH exome

AF:

0.270

GnomAD4 genome

AF:

0.219

AC:

33312

AN:

152110

Hom.:

4130

Cov.:

AF XY:

0.216

AC XY:

16025

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.298

Gnomad4 EAS

AF:

0.290

Gnomad4 SAS

AF:

0.286

Gnomad4 FIN

AF:

0.154

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.276

Hom.:

14731

Bravo

AF:

0.218

Asia WGS

AF:

0.281

AC:

976

AN:

3478

EpiCase

AF:

0.291

EpiControl

AF:

0.294

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

9.9

DANN

Benign

0.78

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over