1-10461512-C-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_004401.3(DFFA):​c.974G>A​(p.Arg325Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,614,002 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 34 hom. )

Consequence

DFFA
NM_004401.3 missense

Scores

2
3
13

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.32
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0036945045).
BP6
Variant 1-10461512-C-T is Benign according to our data. Variant chr1-10461512-C-T is described in ClinVar as [Benign]. Clinvar id is 786715.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00167 (254/152280) while in subpopulation EAS AF = 0.032 (166/5180). AF 95% confidence interval is 0.0281. There are 10 homozygotes in GnomAd4. There are 132 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
BS2
High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DFFANM_004401.3 linkc.974G>A p.Arg325Gln missense_variant Exon 6 of 6 ENST00000377038.8 NP_004392.1 O00273-1
DFFANM_213566.2 linkc.*1522G>A 3_prime_UTR_variant Exon 5 of 5 NP_998731.1 O00273-2A0A024R4H5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DFFAENST00000377038.8 linkc.974G>A p.Arg325Gln missense_variant Exon 6 of 6 1 NM_004401.3 ENSP00000366237.3 O00273-1
DFFAENST00000476658.5 linkn.*374G>A downstream_gene_variant 3 ENSP00000468395.1 K7ERT1

Frequencies

GnomAD3 genomes
AF:
0.00164
AC:
249
AN:
152162
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00190
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0324
Gnomad SAS
AF:
0.00186
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00239
GnomAD2 exomes
AF:
0.00270
AC:
679
AN:
251104
AF XY:
0.00246
show subpopulations
Gnomad AFR exome
AF:
0.000616
Gnomad AMR exome
AF:
0.00162
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0305
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000881
Gnomad OTH exome
AF:
0.00196
GnomAD4 exome
AF:
0.00145
AC:
2114
AN:
1461722
Hom.:
34
Cov.:
31
AF XY:
0.00150
AC XY:
1089
AN XY:
727148
show subpopulations
Gnomad4 AFR exome
AF:
0.000687
AC:
23
AN:
33480
Gnomad4 AMR exome
AF:
0.00139
AC:
62
AN:
44706
Gnomad4 ASJ exome
AF:
0.00
AC:
0
AN:
26124
Gnomad4 EAS exome
AF:
0.0426
AC:
1692
AN:
39688
Gnomad4 SAS exome
AF:
0.00110
AC:
95
AN:
86226
Gnomad4 FIN exome
AF:
0.00
AC:
0
AN:
53410
Gnomad4 NFE exome
AF:
0.0000549
AC:
61
AN:
1111930
Gnomad4 Remaining exome
AF:
0.00295
AC:
178
AN:
60390
Heterozygous variant carriers
0
111
222
333
444
555
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
28
56
84
112
140
<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:
0.00167
AC:
254
AN:
152280
Hom.:
10
Cov.:
32
AF XY:
0.00177
AC XY:
132
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.000770
AC:
0.000769749
AN:
0.000769749
Gnomad4 AMR
AF:
0.00190
AC:
0.00189666
AN:
0.00189666
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.0320
AC:
0.0320463
AN:
0.0320463
Gnomad4 SAS
AF:
0.00186
AC:
0.00186258
AN:
0.00186258
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.0000882
AC:
0.0000882197
AN:
0.0000882197
Gnomad4 OTH
AF:
0.00567
AC:
0.00567108
AN:
0.00567108
Heterozygous variant carriers
0
13
26
39
52
65
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
0.000169
Hom.:
0
Bravo
AF:
0.00180
ESP6500AA
AF:
0.000908
AC:
4
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.00265
AC:
322
Asia WGS
AF:
0.0280
AC:
97
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Aug 15, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
20
DANN
Uncertain
1.0
DEOGEN2
Benign
0.051
T
Eigen
Benign
-0.57
Eigen_PC
Benign
-0.60
FATHMM_MKL
Uncertain
0.80
D
LIST_S2
Benign
0.65
T
MetaRNN
Benign
0.0037
T
MetaSVM
Benign
-0.98
T
MutationAssessor
Uncertain
2.4
M
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.18
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.21
B
Vest4
0.096
MVP
0.27
MPC
0.40
ClinPred
0.079
T
GERP RS
2.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.11
gMVP
0.20
Mutation Taster
=98/2
polymorphism

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.

Other links and lift over

dbSNP: rs140269107; hg19: chr1-10521569; COSMIC: COSV100986620; COSMIC: COSV100986620; API