rs3742837

Variant names:

• chr14-72714848-C-A
• rs3742837
• NM_001280542.3:c.526-347G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-72714848-C-A
• chr14-72714848-C-G
• chr14-72714848-C-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.526-347G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,096 control chromosomes in the GnomAD database, including 42,937 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 0.75 (42937 hom., cov: 32)
• Consequence: DPF3 NM_001280542.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPF3	NM_001280542.3	c.526-347G>T		intron_variant	Intron 5 of 10	ENST00000556509.6	NP_001267471.1
DPF3	NM_001280544.2	c.691-347G>T		intron_variant	Intron 5 of 9		NP_001267473.1
DPF3	NM_001280543.2	c.556-347G>T		intron_variant	Intron 6 of 10		NP_001267472.1
DPF3	NM_012074.5	c.526-347G>T		intron_variant	Intron 5 of 9		NP_036206.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPF3	ENST00000556509.6	c.526-347G>T		intron_variant	Intron 5 of 10	1	NM_001280542.3	ENSP00000450518.1

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114027 AN: 151980 Hom.: 42931 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.750 AC: 114066 AN: 152096 Hom.: 42937 Cov.: 32 AF XY: 0.750 AC XY: 55800 AN XY: 74352

African (AFR) AF: 0.717 AC: 29748 AN: 41480

American (AMR) AF: 0.768 AC: 11733 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3277 AN: 5162

South Asian (SAS) AF: 0.783 AC: 3775 AN: 4822

European-Finnish (FIN) AF: 0.744 AC: 7886 AN: 10600

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52633 AN: 67958

Other (OTH) AF: 0.734 AC: 1551 AN: 2114

Alfa AF: 0.769 Hom.: 72575

Bravo AF: 0.749

Asia WGS AF: 0.721 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3742837; hg19: chr14-73181556;