rs587777425
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP5_ModerateBS2
The NM_015726.4(DCAF8):c.949C>T(p.Arg317Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000958 in 1,566,158 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000099 ( 0 hom. )
Consequence
DCAF8
NM_015726.4 missense
NM_015726.4 missense
Scores
5
10
4
Clinical Significance
Conservation
PhyloP100: 4.41
Genes affected
DCAF8 (HGNC:24891): (DDB1 and CUL4 associated factor 8) This gene encodes a WD repeat-containing protein that interacts with the Cul4-Ddb1 E3 ligase macromolecular complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PP5
Variant 1-160237145-G-A is Pathogenic according to our data. Variant chr1-160237145-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 133348.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCAF8 | NM_015726.4 | c.949C>T | p.Arg317Cys | missense_variant | Exon 6 of 14 | ENST00000368074.6 | NP_056541.2 | |
DCAF8 | NR_028103.2 | n.1482C>T | non_coding_transcript_exon_variant | Exon 6 of 14 | ||||
DCAF8 | NR_028104.2 | n.1408C>T | non_coding_transcript_exon_variant | Exon 5 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000990 AC: 14AN: 1413982Hom.: 0 Cov.: 29 AF XY: 0.00000716 AC XY: 5AN XY: 698594
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Giant axonal neuropathy 2 Pathogenic:1
Mar 11, 2014
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
- -
not provided Pathogenic:1
Dec 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
DCAF8: PP1:Strong, PM2:Supporting, PP2, PS3:Supporting, PS4:Supporting -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;D;.
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M;M;.
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Benign
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
B;B;B;.
Vest4
MVP
MPC
ClinPred
D
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