chr20-57329973-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_012444.3(SPO11):āc.106A>Gā(p.Thr36Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,608,460 control chromosomes in the GnomAD database, including 181 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T36I) has been classified as Uncertain significance.
Frequency
Consequence
NM_012444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPO11 | NM_012444.3 | c.106A>G | p.Thr36Ala | missense_variant | 1/13 | ENST00000371263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPO11 | ENST00000371263.8 | c.106A>G | p.Thr36Ala | missense_variant | 1/13 | 1 | NM_012444.3 | P1 | |
SPO11 | ENST00000345868.8 | c.106A>G | p.Thr36Ala | missense_variant | 1/12 | 1 | |||
SPO11 | ENST00000371260.8 | c.106A>G | p.Thr36Ala | missense_variant | 1/12 | 5 | |||
SPO11 | ENST00000418127.5 | c.40A>G | p.Thr14Ala | missense_variant | 1/10 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0197 AC: 2995AN: 152196Hom.: 81 Cov.: 32
GnomAD3 exomes AF: 0.00532 AC: 1259AN: 236762Hom.: 44 AF XY: 0.00381 AC XY: 493AN XY: 129410
GnomAD4 exome AF: 0.00224 AC: 3258AN: 1456146Hom.: 100 Cov.: 30 AF XY: 0.00191 AC XY: 1383AN XY: 724222
GnomAD4 genome AF: 0.0197 AC: 2998AN: 152314Hom.: 81 Cov.: 32 AF XY: 0.0190 AC XY: 1414AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at