5-10695414-T-C

Position:

• chr5-10695414-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

DAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DAP	NM_004394.3	c.153-11843A>G		intron_variant		ENST00000230895.11	NP_004385.1
DAP	NM_001291963.2	c.153-14245A>G		intron_variant			NP_001278892.1

Ensembl

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

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.518

Alfa AF: 0.404 Hom.: 18862

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

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: rs2930047; hg19: chr5-10695526;