chr2-68157425-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138458.4(DNAAF10):c.19C>T(p.Pro7Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000867 in 1,614,144 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000055 ( 1 hom. )
Consequence
DNAAF10
NM_138458.4 missense
NM_138458.4 missense
Scores
5
7
7
Clinical Significance
Conservation
PhyloP100: 9.16
Genes affected
DNAAF10 (HGNC:25176): (dynein axonemal assembly factor 10) This gene encodes a protein with two WD40 repeat domains thought to be involved in an apoptosis via activation of caspase-3. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14787754).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF10 | NM_138458.4 | c.19C>T | p.Pro7Ser | missense_variant | 1/8 | ENST00000295121.11 | NP_612467.1 | |
DNAAF10 | NM_001256476.2 | c.19C>T | p.Pro7Ser | missense_variant | 1/7 | NP_001243405.1 | ||
DNAAF10 | NR_046234.2 | n.103C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF10 | ENST00000295121.11 | c.19C>T | p.Pro7Ser | missense_variant | 1/8 | 1 | NM_138458.4 | ENSP00000295121.6 | ||
ENSG00000273398 | ENST00000406334.3 | n.*36C>T | non_coding_transcript_exon_variant | 8/15 | 2 | ENSP00000384974.3 | ||||
ENSG00000273398 | ENST00000406334.3 | n.*36C>T | 3_prime_UTR_variant | 8/15 | 2 | ENSP00000384974.3 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152140Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000131 AC: 33AN: 251372Hom.: 1 AF XY: 0.000125 AC XY: 17AN XY: 135886
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GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461886Hom.: 1 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727244
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GnomAD4 genome AF: 0.000387 AC: 59AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74448
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.19C>T (p.P7S) alteration is located in exon 1 (coding exon 1) of the WDR92 gene. This alteration results from a C to T substitution at nucleotide position 19, causing the proline (P) at amino acid position 7 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Uncertain
T;T
Polyphen
D;.
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