Genetic Variant DAP:c.*171C>T (chr5-10680885-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004394.3(DAP):c.*171C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 1,536,988 control chromosomes in the GnomAD database, including 4,757 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 0.056 ( 321 hom., cov: 33)

Exomes 𝑓: 0.077 ( 4436 hom. )

Consequence

DAP
NM_004394.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.600

Publications

28 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024189353).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAP	NM_004394.3 link	c.*171C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000230895.11	NP_004385.1	P51397
DAP	NM_001291963.2 link	c.437C>T	p.Ser146Phe	missense_variant	Exon 3 of 3		NP_001278892.1	P51397B4DQ75

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DAP	ENST00000230895.11 link	c.*171C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_004394.3	ENSP00000230895.7	P51397
DAP	ENST00000432074.2 link	c.437C>T	p.Ser146Phe	missense_variant	Exon 3 of 3	2		ENSP00000394163.2	B4DQ75
DAP	ENST00000514882.5 link	n.*206C>T		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0561

AC:

8540

AN:

152178

Hom.:

321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0163

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0744

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0850

Gnomad OTH

AF:

0.0617

GnomAD2 exomes

AF:

0.0553

AC:

8016

AN:

144910

AF XY:

0.0549

show subpopulations

Gnomad AFR exome

AF:

0.0129

Gnomad AMR exome

AF:

0.0443

Gnomad ASJ exome

AF:

0.0554

Gnomad EAS exome

AF:

0.00178

Gnomad FIN exome

AF:

0.0753

Gnomad NFE exome

AF:

0.0859

Gnomad OTH exome

AF:

0.0700

GnomAD4 exome

AF:

0.0769

AC:

106416

AN:

1384692

Hom.:

4436

Cov.:

AF XY:

0.0754

AC XY:

51541

AN XY:

683264

show subpopulations

African (AFR)

AF:

0.0110

AC:

346

AN:

31594

American (AMR)

AF:

0.0458

AC:

1635

AN:

35700

Ashkenazi Jewish (ASJ)

AF:

0.0570

AC:

1436

AN:

25182

East Asian (EAS)

AF:

0.000558

AC:

AN:

35872

South Asian (SAS)

AF:

0.0197

AC:

1559

AN:

79236

European-Finnish (FIN)

AF:

0.0803

AC:

2771

AN:

34494

Middle Eastern (MID)

AF:

0.0481

AC:

274

AN:

5698

European-Non Finnish (NFE)

AF:

0.0875

AC:

94431

AN:

1078924

Other (OTH)

AF:

0.0680

AC:

3944

AN:

57992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

5896

11793

17689

23586

29482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0561

AC:

8537

AN:

152296

Hom.:

321

Cov.:

AF XY:

0.0537

AC XY:

3999

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.0163

AC:

676

AN:

41568

American (AMR)

AF:

0.0503

AC:

770

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0536

AC:

186

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0195

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0744

AC:

789

AN:

10600

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0850

AC:

5782

AN:

68028

Other (OTH)

AF:

0.0610

AC:

129

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

421

842

1264

1685

2106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0709

Hom.:

392

Bravo

AF:

0.0526

TwinsUK

AF:

0.0850

AC:

315

ALSPAC

AF:

0.0864

AC:

333

ExAC

AF:

0.0346

AC:

1104

Asia WGS

AF:

0.00808

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.39

CADD

Benign

5.0

(source)

DANN

Uncertain

1.0

Eigen

Benign

-0.031

Eigen_PC

Benign

-0.22

FATHMM_MKL

Benign

0.057

LIST_S2

Benign

0.55

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.76

PhyloP100

0.60

PROVEAN

Benign

-0.60

REVEL

Benign

0.10

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.077

ClinPred

0.015

GERP RS

3.7

gMVP

0.011

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr5-10680885-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over