2-68134771-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_138458.4(DNAAF10):​c.797G>A​(p.Arg266Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,611,182 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

DNAAF10
NM_138458.4 missense

Scores

2
10
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.05
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAAF10NM_138458.4 linkc.797G>A p.Arg266Gln missense_variant Exon 7 of 8 ENST00000295121.11 NP_612467.1 Q96MX6-1A0A140VK67
DNAAF10NM_001256476.2 linkc.797G>A p.Arg266Gln missense_variant Exon 7 of 7 NP_001243405.1 Q96MX6-2
DNAAF10NR_046234.2 linkn.768G>A non_coding_transcript_exon_variant Exon 7 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAAF10ENST00000295121.11 linkc.797G>A p.Arg266Gln missense_variant Exon 7 of 8 1 NM_138458.4 ENSP00000295121.6 Q96MX6-1
ENSG00000273398ENST00000406334.3 linkn.*814G>A non_coding_transcript_exon_variant Exon 14 of 15 2 ENSP00000384974.3 H7BYZ3
ENSG00000273398ENST00000406334.3 linkn.*814G>A 3_prime_UTR_variant Exon 14 of 15 2 ENSP00000384974.3 H7BYZ3

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152148
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1459034
Hom.:
0
Cov.:
31
AF XY:
0.00000276
AC XY:
2
AN XY:
725852
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152148
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 01, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.797G>A (p.R266Q) alteration is located in exon 7 (coding exon 7) of the WDR92 gene. This alteration results from a G to A substitution at nucleotide position 797, causing the arginine (R) at amino acid position 266 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Uncertain
0.12
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.011
T;.;.
Eigen
Uncertain
0.38
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.97
D;D;D
M_CAP
Benign
0.047
D
MetaRNN
Uncertain
0.55
D;D;D
MetaSVM
Uncertain
0.062
D
MutationAssessor
Uncertain
2.5
M;.;M
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-2.3
N;N;N
REVEL
Uncertain
0.34
Sift
Benign
0.054
T;T;T
Sift4G
Benign
0.23
T;T;T
Polyphen
0.92
P;.;.
Vest4
0.79
MutPred
0.62
Loss of MoRF binding (P = 0.0144);.;Loss of MoRF binding (P = 0.0144);
MVP
0.69
MPC
0.39
ClinPred
0.97
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.30
gMVP
0.53

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: rs1007173839; hg19: chr2-68361903; API