5-10701402-A-G

Variant names:

• chr5-10701402-A-G
• rs3756407
• NM_004394.3:c.153-17831T>C

Variant summary

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

The NM_004394.3(DAP):​c.153-17831T>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
• Publications: 4 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=-0.87).
• 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 rank	MANE	Protein	UniProt
DAP	NM_004394.3	c.153-17831T>C		intron_variant	Intron 2 of 3	ENST00000230895.11	NP_004385.1
DAP	NM_001291963.2	c.153-20233T>C		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.153-17831T>C		intron_variant	Intron 2 of 3	1	NM_004394.3	ENSP00000230895.7
DAP	ENST00000432074.2	c.153-20233T>C		intron_variant	Intron 2 of 2	2		ENSP00000394163.2
DAP	ENST00000508253.5	n.310-17831T>C		intron_variant	Intron 2 of 2	2
DAP	ENST00000514882.5	n.221-17831T>C		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.113 AC: 4684 AN: 41516

American (AMR) AF: 0.0577 AC: 882 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1017 AN: 5184

South Asian (SAS) AF: 0.128 AC: 616 AN: 4814

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10624

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0297 AC: 2023 AN: 68020

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0453 Hom.: 337

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
PhyloP100		-1.3
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: rs3756407; hg19: chr5-10701514;