dbSNP rs267927: DAP:c.-2T>C (chr5-10761070-A-G) – 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.-2T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.981 in 1,218,190 control chromosomes in the GnomAD database, including 588,041 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 0.97 ( 70881 hom., cov: 31)

Exomes 𝑓: 0.98 ( 517160 hom. )

Consequence

DAP
NM_004394.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Publications

9 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:

DAP-DT (HGNC:55214): (DAP divergent transcript)

DAP-DT 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 (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DAP	NM_004394.3 link	c.-2T>C	5_prime_UTR_variant	Exon 1 of 4	ENST00000230895.11	NP_004385.1	P51397
DAP-DT	NR_187555.1 link	n.35A>G	non_coding_transcript_exon_variant	Exon 1 of 3
DAP	NM_001291963.2 link	c.-2T>C	5_prime_UTR_variant	Exon 1 of 3		NP_001278892.1	P51397B4DQ75

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAP	ENST00000230895.11 link	c.-2T>C		5_prime_UTR_variant	Exon 1 of 4	1	NM_004394.3	ENSP00000230895.7		P51397

Frequencies

GnomAD3 genomes

AF:

0.970

AC:

145432

AN:

149992

Hom.:

70827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.979

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.958

Gnomad ASJ

AF:

0.998

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.844

Gnomad FIN

AF:

0.980

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.996

Gnomad OTH

AF:

0.968

GnomAD2 exomes

AF:

0.946

AC:

56027

AN:

59220

AF XY:

0.947

show subpopulations

Gnomad AFR exome

AF:

0.973

Gnomad AMR exome

AF:

0.905

Gnomad ASJ exome

AF:

0.997

Gnomad EAS exome

AF:

0.614

Gnomad FIN exome

AF:

0.981

Gnomad NFE exome

AF:

0.994

Gnomad OTH exome

AF:

0.959

GnomAD4 exome

AF:

0.982

AC:

1049264

AN:

1068092

Hom.:

517160

Cov.:

AF XY:

0.982

AC XY:

499365

AN XY:

508548

show subpopulations

African (AFR)

AF:

0.978

AC:

21534

AN:

22024

American (AMR)

AF:

0.925

AC:

8705

AN:

9414

Ashkenazi Jewish (ASJ)

AF:

0.998

AC:

11662

AN:

11682

East Asian (EAS)

AF:

0.646

AC:

15528

AN:

24026

South Asian (SAS)

AF:

0.851

AC:

18897

AN:

22208

European-Finnish (FIN)

AF:

0.983

AC:

34179

AN:

34780

Middle Eastern (MID)

AF:

0.983

AC:

2629

AN:

2674

European-Non Finnish (NFE)

AF:

0.996

AC:

897321

AN:

901010

Other (OTH)

AF:

0.964

AC:

38809

AN:

40274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

638

1275

1913

2550

3188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20770

41540

62310

83080

103850

<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:

0.970

AC:

145539

AN:

150098

Hom.:

70881

Cov.:

AF XY:

0.965

AC XY:

70652

AN XY:

73236

show subpopulations

African (AFR)

AF:

0.979

AC:

40424

AN:

41290

American (AMR)

AF:

0.958

AC:

14494

AN:

15134

Ashkenazi Jewish (ASJ)

AF:

0.998

AC:

3422

AN:

3428

East Asian (EAS)

AF:

0.660

AC:

3343

AN:

5066

South Asian (SAS)

AF:

0.843

AC:

4063

AN:

4818

European-Finnish (FIN)

AF:

0.980

AC:

9667

AN:

9866

Middle Eastern (MID)

AF:

0.990

AC:

289

AN:

292

European-Non Finnish (NFE)

AF:

0.996

AC:

66909

AN:

67210

Other (OTH)

AF:

0.968

AC:

2018

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

195

390

585

780

975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.987

Hom.:

10351

Asia WGS

AF:

0.790

AC:

2462

AN:

3114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.12

PromoterAI

0.11

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=299/1

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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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