chr17-50550039-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022827.4(SPATA20):c.917G>C(p.Gly306Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000415 in 1,445,642 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000042 ( 0 hom. )
Consequence
SPATA20
NM_022827.4 missense
NM_022827.4 missense
Scores
1
5
8
Clinical Significance
Conservation
PhyloP100: 9.86
Genes affected
SPATA20 (HGNC:26125): (spermatogenesis associated 20) Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.32154658).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA20 | NM_022827.4 | c.917G>C | p.Gly306Ala | missense_variant | 8/17 | ENST00000006658.11 | |
SPATA20 | NM_001258372.2 | c.869G>C | p.Gly290Ala | missense_variant | 7/16 | ||
SPATA20 | NM_001258373.2 | c.737G>C | p.Gly246Ala | missense_variant | 8/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA20 | ENST00000006658.11 | c.917G>C | p.Gly306Ala | missense_variant | 8/17 | 1 | NM_022827.4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445642Hom.: 0 Cov.: 32 AF XY: 0.00000279 AC XY: 2AN XY: 716208
GnomAD4 exome
AF:
AC:
6
AN:
1445642
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
716208
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
Bravo
AF:
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 | Oct 10, 2023 | The c.917G>C (p.G306A) alteration is located in exon 8 (coding exon 8) of the SPATA20 gene. This alteration results from a G to C substitution at nucleotide position 917, causing the glycine (G) at amino acid position 306 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T;T
Polyphen
0.020, 0.085
.;B;B;.
Vest4
MutPred
0.19
.;.;Gain of MoRF binding (P = 0.1448);Gain of MoRF binding (P = 0.1448);
MVP
MPC
0.42
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