20-57331913-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012444.3(SPO11):c.212C>T(p.Thr71Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00006 in 1,598,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPO11 | ENST00000371263.8 | c.212C>T | p.Thr71Met | missense_variant | 2/13 | 1 | NM_012444.3 | ENSP00000360310.3 | ||
SPO11 | ENST00000345868.8 | c.132-1275C>T | intron_variant | 1 | ENSP00000316034.4 | |||||
SPO11 | ENST00000418127.5 | c.146C>T | p.Thr49Met | missense_variant | 2/10 | 3 | ENSP00000413185.1 | |||
SPO11 | ENST00000371260.8 | c.132-1275C>T | intron_variant | 5 | ENSP00000360307.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000656 AC: 16AN: 243918Hom.: 0 AF XY: 0.0000455 AC XY: 6AN XY: 131920
GnomAD4 exome AF: 0.0000643 AC: 93AN: 1446794Hom.: 0 Cov.: 29 AF XY: 0.0000598 AC XY: 43AN XY: 719356
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2024 | The c.212C>T (p.T71M) alteration is located in exon 2 (coding exon 2) of the SPO11 gene. This alteration results from a C to T substitution at nucleotide position 212, causing the threonine (T) at amino acid position 71 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at