5-10752203-C-T

Variant names:

• chr5-10752203-C-T
• rs267939
• NM_004394.3:c.56-3932G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 37 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004394.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAP	NM_004394.3	MANE Select	c.56-3932G>A		intron	N/A	NP_004385.1
	DAP	NM_001291963.2		c.56-3932G>A		intron	N/A	NP_001278892.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAP	ENST00000230895.11	TSL:1 MANE Select	c.56-3932G>A		intron	N/A	ENSP00000230895.7
	DAP	ENST00000432074.2	TSL:2	c.56-3932G>A		intron	N/A	ENSP00000394163.2
	DAP	ENST00000508253.5	TSL:2	n.213-3932G>A		intron	N/A

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

African (AFR) AF: 0.269 AC: 11172 AN: 41524

American (AMR) AF: 0.511 AC: 7813 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3472

East Asian (EAS) AF: 0.126 AC: 652 AN: 5188

South Asian (SAS) AF: 0.314 AC: 1516 AN: 4822

European-Finnish (FIN) AF: 0.693 AC: 7340 AN: 10596

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43234 AN: 67996

Other (OTH) AF: 0.477 AC: 1008 AN: 2112

Alfa AF: 0.583 Hom.: 112184

Bravo AF: 0.471

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.73
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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: rs267939; hg19: chr5-10752315;