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. Variant got -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

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

Verdict is Likely_benign. Variant got -2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.871+11177G>C		intron_variant	Intron 8 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.*1185-230G>C		intron_variant	Intron 9 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.*1185-230G>C		intron_variant	Intron 10 of 10		NP_001267472.1
DPF3	NM_012074.5	c.*1185-230G>C		intron_variant	Intron 9 of 9		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.871+11177G>C		intron_variant	Intron 8 of 10	1	NM_001280542.3	ENSP00000450518.1

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 v4.3

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

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

Other links and lift over

dbSNP: rs1381; hg19: chr14-73129771;