dbSNP rs9857: DAP:c.*621A>G (chr5-10680435-T-C) – 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.*621A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 418,666 control chromosomes in the GnomAD database, including 18,649 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 0.31 ( 7783 hom., cov: 33)

Exomes 𝑓: 0.28 ( 10866 hom. )

Consequence

DAP
NM_004394.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.321

Publications

16 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 (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAP	NM_004394.3 link	c.*621A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000230895.11	NP_004385.1
DAP	NM_001291963.2 link	c.*272A>G		3_prime_UTR_variant	Exon 3 of 3		NP_001278892.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
DAP	ENST00000230895.11 link	c.*621A>G	3_prime_UTR_variant	Exon 4 of 4	1	NM_004394.3	ENSP00000230895.7
DAP	ENST00000432074.2 link	c.*272A>G	splice_region_variant	Exon 3 of 3	2		ENSP00000394163.2
DAP	ENST00000432074.2 link	c.*272A>G	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000394163.2

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46969

AN:

152004

Hom.:

7765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.311

GnomAD4 exome

AF:

0.276

AC:

73444

AN:

266544

Hom.:

10866

Cov.:

AF XY:

0.279

AC XY:

38721

AN XY:

139024

show subpopulations

African (AFR)

AF:

0.397

AC:

3153

AN:

7942

American (AMR)

AF:

0.273

AC:

2401

AN:

8798

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

2226

AN:

8932

East Asian (EAS)

AF:

0.419

AC:

7106

AN:

16946

South Asian (SAS)

AF:

0.335

AC:

8686

AN:

25966

European-Finnish (FIN)

AF:

0.187

AC:

2680

AN:

14300

Middle Eastern (MID)

AF:

0.385

AC:

467

AN:

1212

European-Non Finnish (NFE)

AF:

0.254

AC:

42287

AN:

166410

Other (OTH)

AF:

0.277

AC:

4438

AN:

16038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2453

4907

7360

9814

12267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

318

636

954

1272

1590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.309

AC:

47019

AN:

152122

Hom.:

7783

Cov.:

AF XY:

0.308

AC XY:

22902

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.412

AC:

17104

AN:

41488

American (AMR)

AF:

0.284

AC:

4338

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.259

AC:

898

AN:

3472

East Asian (EAS)

AF:

0.447

AC:

2310

AN:

5168

South Asian (SAS)

AF:

0.373

AC:

1801

AN:

4822

European-Finnish (FIN)

AF:

0.195

AC:

2069

AN:

10596

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17383

AN:

67972

Other (OTH)

AF:

0.318

AC:

670

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1624

3249

4873

6498

8122

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.275

Hom.:

10217

Bravo

AF:

0.318

Asia WGS

AF:

0.434

AC:

1509

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

6.5

(source)

DANN

Benign

0.48

PhyloP100

-0.32

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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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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