rs5745297
Positions:
Variant summary
Our verdict is Benign. Variant got -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
NM_004394.3 3_prime_UTR
Scores
2
1
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.600
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]
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 | UniProt |
---|---|---|---|---|---|---|---|
DAP | NM_004394.3 | c.*171C>T | 3_prime_UTR_variant | 4/4 | ENST00000230895.11 | ||
DAP | NM_001291963.2 | c.437C>T | p.Ser146Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAP | ENST00000230895.11 | c.*171C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_004394.3 | P1 | ||
DAP | ENST00000432074.2 | c.437C>T | p.Ser146Phe | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0561 AC: 8540AN: 152178Hom.: 321 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
8540
AN:
152178
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0553 AC: 8016AN: 144910Hom.: 320 AF XY: 0.0549 AC XY: 4244AN XY: 77320
GnomAD3 exomes
AF:
AC:
8016
AN:
144910
Hom.:
AF XY:
AC XY:
4244
AN XY:
77320
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0769 AC: 106416AN: 1384692Hom.: 4436 Cov.: 32 AF XY: 0.0754 AC XY: 51541AN XY: 683264
GnomAD4 exome
AF:
AC:
106416
AN:
1384692
Hom.:
Cov.:
32
AF XY:
AC XY:
51541
AN XY:
683264
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0561 AC: 8537AN: 152296Hom.: 321 Cov.: 33 AF XY: 0.0537 AC XY: 3999AN XY: 74464
GnomAD4 genome
?
AF:
AC:
8537
AN:
152296
Hom.:
Cov.:
33
AF XY:
AC XY:
3999
AN XY:
74464
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
315
ALSPAC
AF:
AC:
333
ExAC
?
AF:
AC:
1104
Asia WGS
AF:
AC:
28
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
ClinPred
T
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at