chr20-57331862-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_012444.3(SPO11):c.161T>C(p.Ile54Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SPO11
NM_012444.3 missense
NM_012444.3 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 5.17
Publications
0 publications found
Genes affected
SPO11 (HGNC:11250): (SPO11 initiator of meiotic double strand breaks) Meiotic recombination and chromosome segregation require the formation of double-strand breaks (DSBs) in paired chromosome homologs. During meiosis in yeast, a meiotic recombination protein is covalently-linked to the 5' end of DSBs and is essential for the formation of DSBs. The protein encoded by this gene is similar in sequence and conserved features to the yeast meiotic recombination protein. The encoded protein belongs to the TOP6A protein family. Several transcript variants encoding different isoforms have been found for this gene, but the full-length nature of only two of them have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34747553).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012444.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SPO11 | TSL:1 MANE Select | c.161T>C | p.Ile54Thr | missense | Exon 2 of 13 | ENSP00000360310.3 | Q9Y5K1-1 | ||
| SPO11 | TSL:1 | c.132-1326T>C | intron | N/A | ENSP00000316034.4 | Q9Y5K1-2 | |||
| SPO11 | TSL:3 | c.95T>C | p.Ile32Thr | missense | Exon 2 of 10 | ENSP00000413185.1 | Q5TCH6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1446950Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 719566
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1446950
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
719566
African (AFR)
AF:
AC:
0
AN:
33010
American (AMR)
AF:
AC:
0
AN:
43052
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25786
East Asian (EAS)
AF:
AC:
0
AN:
39236
South Asian (SAS)
AF:
AC:
0
AN:
82766
European-Finnish (FIN)
AF:
AC:
0
AN:
52900
Middle Eastern (MID)
AF:
AC:
0
AN:
5726
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1104726
Other (OTH)
AF:
AC:
0
AN:
59748
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of stability (P = 0.0051)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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