17-3467540-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001170698.2(SPATA22):c.58C>T(p.Pro20Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000997 in 1,604,512 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
SPATA22
NM_001170698.2 missense
NM_001170698.2 missense
Scores
7
8
4
Clinical Significance
Conservation
PhyloP100: 6.61
Genes affected
SPATA22 (HGNC:30705): (spermatogenesis associated 22) Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]
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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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA22 | NM_001170698.2 | c.58C>T | p.Pro20Ser | missense_variant | 3/9 | ENST00000572969.6 | NP_001164169.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA22 | ENST00000572969.6 | c.58C>T | p.Pro20Ser | missense_variant | 3/9 | 1 | NM_001170698.2 | ENSP00000460187 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000569 AC: 14AN: 246248Hom.: 0 AF XY: 0.0000602 AC XY: 8AN XY: 132994
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GnomAD4 exome AF: 0.00000964 AC: 14AN: 1452592Hom.: 0 Cov.: 30 AF XY: 0.00000969 AC XY: 7AN XY: 722204
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74192
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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 | Nov 08, 2022 | The c.58C>T (p.P20S) alteration is located in exon 3 (coding exon 2) of the SPATA22 gene. This alteration results from a C to T substitution at nucleotide position 58, causing the proline (P) at amino acid position 20 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
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T;T;T;.;.;T;T;.
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;.;D;D;D;T;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;.;M;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.;.;.;D;D;.;.;.
REVEL
Uncertain
Sift
Pathogenic
D;.;.;.;D;D;.;.;.
Sift4G
Pathogenic
D;D;D;D;D;D;.;D;.
Polyphen
D;D;D;D;D;.;.;.;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);.;Gain of MoRF binding (P = 0.0325);Gain of MoRF binding (P = 0.0325);
MVP
MPC
0.21
ClinPred
D
GERP RS
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gMVP
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at