rs7255123

Variant names:

• chr19-3958399-A-C
• rs7255123
• ENST00000723280.1:n.1768-2239A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-3958399-A-C
• chr19-3958399-A-G

Variant summary

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

The ENST00000723280.1(ENSG00000294388):​n.1768-2239A>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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000294388 ENST00000723280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 13 publications found

Genes affected

ENSG00000294388 (HGNC:):

DAPK3 (HGNC:2676): (death associated protein kinase 3) Death-associated protein kinase 3 (DAPK3) induces morphological changes in apoptosis when overexpressed in mammalian cells. These results suggest that DAPK3 may play a role in the induction of apoptosis. [provided by RefSeq, Jul 2008]

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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723280.1. 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
	DAPK3	NM_001348.3	MANE Select	c.*702T>G		downstream_gene	N/A	NP_001339.1	O43293-1
	DAPK3	NM_001375658.1		c.*702T>G		downstream_gene	N/A	NP_001362587.1	O43293-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294388	ENST00000723280.1		n.1768-2239A>C		intron	N/A
	DAPK3	ENST00000545797.7	TSL:2 MANE Select	c.*702T>G		downstream_gene	N/A	ENSP00000442973.1	O43293-1
	DAPK3	ENST00000301264.7	TSL:1	c.*702T>G		downstream_gene	N/A	ENSP00000301264.3	O43293-1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 303854 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 173020

African (AFR) AF: 0.00 AC: 0 AN: 8628

American (AMR) AF: 0.00 AC: 0 AN: 27262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10772

East Asian (EAS) AF: 0.00 AC: 0 AN: 9208

South Asian (SAS) AF: 0.00 AC: 0 AN: 59744

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12362

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2780

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158876

Other (OTH) AF: 0.00 AC: 0 AN: 14222

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 75207

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7255123;

hg19: chr19-3958397;