Variant rs5745297 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001291963.2(DAP):c.437C>T(p.Ser146Phe) variant causes a missense 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. 10/13 in silico tools predict 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_001291963.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.600

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DAP	NM_004394.3 linkuse as main transcript	c.*171C>T		3_prime_UTR_variant	4/4	ENST00000230895.11	NP_004385.1	P51397
DAP	NM_001291963.2 linkuse as main transcript	c.437C>T	p.Ser146Phe	missense_variant	3/3		NP_001278892.1	P51397B4DQ75

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAP	ENST00000230895.11 linkuse as main transcript	c.*171C>T		3_prime_UTR_variant	4/4	1	NM_004394.3	ENSP00000230895.7		P51397
DAP	ENST00000432074.2 linkuse as main transcript	c.437C>T	p.Ser146Phe	missense_variant	3/3	2		ENSP00000394163.2		B4DQ75

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

GnomAD3 exomes

AF:

0.0553

AC:

8016

AN:

144910

Hom.:

320

AF XY:

0.0549

AC XY:

4244

AN XY:

77320

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 SAS exome

AF:

0.0183

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

Gnomad4 AFR exome

AF:

0.0110

Gnomad4 AMR exome

AF:

0.0458

Gnomad4 ASJ exome

AF:

0.0570

Gnomad4 EAS exome

AF:

0.000558

Gnomad4 SAS exome

AF:

0.0197

Gnomad4 FIN exome

AF:

0.0803

Gnomad4 NFE exome

AF:

0.0875

Gnomad4 OTH exome

AF:

0.0680

GnomAD4 genome

AF:

0.0561

AC:

8537

AN:

152296

Hom.:

321

Cov.:

AF XY:

0.0537

AC XY:

3999

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0163

Gnomad4 AMR

AF:

0.0503

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0195

Gnomad4 FIN

AF:

0.0744

Gnomad4 NFE

AF:

0.0850

Gnomad4 OTH

AF:

0.0610

Alfa

AF:

0.0730

Hom.:

310

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

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

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over