rs1381

Variant names:

• chr14-72663063-C-G
• rs1381
• NM_001280542.3:c.871+11177G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-72663063-C-G
• chr14-72663063-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001280542.3(DPF3):​c.871+11177G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 27)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001280542.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPF3	NM_001280542.3	MANE Select	c.871+11177G>C		intron	N/A	NP_001267471.1	Q92784-1
	DPF3	NM_001280544.2		c.*1185-230G>C		intron	N/A	NP_001267473.1	F8W7T1
	DPF3	NM_001280543.2		c.*1185-230G>C		intron	N/A	NP_001267472.1	Q92784-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPF3	ENST00000556509.6	TSL:1 MANE Select	c.871+11177G>C		intron	N/A	ENSP00000450518.1	Q92784-1
	DPF3	ENST00000381216.8	TSL:1	n.*1185-230G>C		intron	N/A	ENSP00000370614.4	Q92784-2
	DPF3	ENST00000366353.8	TSL:2	n.*1185-230G>C		intron	N/A	ENSP00000381791.3	F8W7T1

Frequencies

GnomAD3 genomes Cov.: 27

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

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		1.4

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: rs1381; hg19: chr14-73129771;