rs267939

chr5-10752203-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004394.3(DAP):c.56-3932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,202 control chromosomes in the GnomAD database, including 21,125 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 0.49 (21125 hom., cov: 34)
• Consequence: DAP NM_004394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

DAP (HGNC:2672): (death associated protein) This gene encodes a basic, proline-rich, 15-kD protein. The protein acts as a positive mediator of programmed cell death that is induced by interferon-gamma. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAP	NM_004394.3	c.56-3932G>A		intron_variant		ENST00000230895.11
DAP	NM_001291963.2	c.56-3932G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAP	ENST00000230895.11	c.56-3932G>A		intron_variant		1	NM_004394.3	P1

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75248 AN: 152084 Hom.: 21128 Cov.: 34

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.494 AC: 75248 AN: 152202 Hom.: 21125 Cov.: 34 AF XY: 0.492 AC XY: 36613 AN XY: 74400

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.477

Alfa AF: 0.593 Hom.: 57758

Bravo AF: 0.471

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.4
Dann	Benign	0.73

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: rs267939; hg19: chr5-10752315;