rs3756407

chr5-10701402-A-G

Variant summary

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

The NM_004394.3(DAP):c.153-17831T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,242 control chromosomes in the GnomAD database, including 484 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 0.063 (484 hom., cov: 32)
• Consequence: DAP NM_004394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAP	NM_004394.3	c.153-17831T>C		intron_variant		ENST00000230895.11
DAP	NM_001291963.2	c.153-20233T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAP	ENST00000230895.11	c.153-17831T>C		intron_variant		1	NM_004394.3	P1
DAP	ENST00000432074.2	c.153-20233T>C		intron_variant		2
DAP	ENST00000508253.5	n.310-17831T>C		intron_variant, non_coding_transcript_variant		2
DAP	ENST00000514882.5	n.221-17831T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9543 AN: 152124 Hom.: 479 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0629 AC: 9582 AN: 152242 Hom.: 484 Cov.: 32 AF XY: 0.0645 AC XY: 4804 AN XY: 74450

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.00819

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0395 Hom.: 163

Bravo AF: 0.0686

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.44
Dann	Benign	0.41

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: rs3756407; hg19: chr5-10701514;