NM_004394.3:c.153-11843A>G

Variant names:

• chr5-10695414-T-C
• rs2930047
• NM_004394.3:c.153-11843A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004394.3(DAP):​c.153-11843A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,176 control chromosomes in the GnomAD database, including 20,752 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 0.50 (20752 hom., cov: 33)
• Consequence: DAP NM_004394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 50 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAP	NM_004394.3	c.153-11843A>G		intron_variant	Intron 2 of 3	ENST00000230895.11	NP_004385.1
DAP	NM_001291963.2	c.153-14245A>G		intron_variant	Intron 2 of 2		NP_001278892.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAP	ENST00000230895.11	c.153-11843A>G		intron_variant	Intron 2 of 3	1	NM_004394.3	ENSP00000230895.7
DAP	ENST00000432074.2	c.153-14245A>G		intron_variant	Intron 2 of 2	2		ENSP00000394163.2
DAP	ENST00000508253.5	n.310-11843A>G		intron_variant	Intron 2 of 2	2
DAP	ENST00000514882.5	n.221-11843A>G		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75391 AN: 152058 Hom.: 20699 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.496 AC: 75505 AN: 152176 Hom.: 20752 Cov.: 33 AF XY: 0.496 AC XY: 36930 AN XY: 74384

African (AFR) AF: 0.706 AC: 29323 AN: 41524

American (AMR) AF: 0.471 AC: 7199 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1548 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3860 AN: 5170

South Asian (SAS) AF: 0.667 AC: 3218 AN: 4828

European-Finnish (FIN) AF: 0.296 AC: 3134 AN: 10586

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25536 AN: 67984

Other (OTH) AF: 0.518 AC: 1094 AN: 2110

Alfa AF: 0.421 Hom.: 51946

Bravo AF: 0.516

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.49
PhyloP100		-0.20
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: rs2930047; hg19: chr5-10695526;