chr14-72846718-A-G

Variant names:

• chr14-72846718-A-G
• rs8010957
• NM_001280542.3:c.32+47339T>C

Variant summary

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

The NM_001280542.3(DPF3):​c.32+47339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.974 in 152,072 control chromosomes in the GnomAD database, including 72,144 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 0.97 (72144 hom., cov: 29)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.32+47339T>C		intron_variant	Intron 1 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.197+45429T>C		intron_variant	Intron 1 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.62+33086T>C		intron_variant	Intron 2 of 10		NP_001267472.1
DPF3	NM_012074.5	c.32+47339T>C		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.32+47339T>C		intron_variant	Intron 1 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.974 AC: 147960 AN: 151954 Hom.: 72081 Cov.: 29

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.974 AC: 148082 AN: 152072 Hom.: 72144 Cov.: 29 AF XY: 0.973 AC XY: 72303 AN XY: 74312

African (AFR) AF: 0.991 AC: 41114 AN: 41488

American (AMR) AF: 0.970 AC: 14792 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3238 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5148 AN: 5148

South Asian (SAS) AF: 0.991 AC: 4766 AN: 4808

European-Finnish (FIN) AF: 0.955 AC: 10090 AN: 10570

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65787 AN: 68020

Other (OTH) AF: 0.970 AC: 2042 AN: 2106

Alfa AF: 0.968 Hom.: 4229

Bravo AF: 0.976

Asia WGS AF: 0.994 AC: 3455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.29
PhyloP100		-3.1
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: rs8010957; hg19: chr14-73313426;