1-10463569-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004401.3(DFFA):c.493T>C(p.Cys165Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00243 in 1,614,202 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 17 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 26 hom. )
Consequence
DFFA
NM_004401.3 missense
NM_004401.3 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 0.656
Genes affected
DFFA (HGNC:2772): (DNA fragmentation factor subunit alpha) Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. DFF becomes activated when DFFA is cleaved by caspase-3. The cleaved fragments of DFFA dissociate from DFFB, the active component of DFF. DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002888918).
BP6
?
Variant 1-10463569-A-G is Benign according to our data. Variant chr1-10463569-A-G is described in ClinVar as [Benign]. Clinvar id is 777880.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00817 (1245/152332) while in subpopulation AFR AF= 0.0246 (1024/41578). AF 95% confidence interval is 0.0234. There are 17 homozygotes in gnomad4. There are 602 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DFFA | NM_004401.3 | c.493T>C | p.Cys165Arg | missense_variant | 4/6 | ENST00000377038.8 | |
DFFA | NM_213566.2 | c.493T>C | p.Cys165Arg | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DFFA | ENST00000377038.8 | c.493T>C | p.Cys165Arg | missense_variant | 4/6 | 1 | NM_004401.3 | P1 | |
DFFA | ENST00000377036.2 | c.493T>C | p.Cys165Arg | missense_variant | 4/5 | 1 | |||
DFFA | ENST00000476658.5 | c.442-360T>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00817 AC: 1244AN: 152214Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00317 AC: 796AN: 251218Hom.: 9 AF XY: 0.00271 AC XY: 368AN XY: 135772
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GnomAD4 exome AF: 0.00183 AC: 2681AN: 1461870Hom.: 26 Cov.: 31 AF XY: 0.00175 AC XY: 1273AN XY: 727238
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GnomAD4 genome ? AF: 0.00817 AC: 1245AN: 152332Hom.: 17 Cov.: 32 AF XY: 0.00808 AC XY: 602AN XY: 74490
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ESP6500AA
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Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 02, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at