chr13-24223508-C-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001166271.3(SPATA13):c.579C>A(p.Phe193Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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)
Consequence
SPATA13
NM_001166271.3 missense
NM_001166271.3 missense
Scores
2
3
7
Clinical Significance
Conservation
PhyloP100: 0.323
Genes affected
SPATA13 (HGNC:23222): (spermatogenesis associated 13) Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [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=0.31640655).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.579C>A | p.Phe193Leu | missense_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.765C>A | p.Phe255Leu | missense_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-25969C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.579C>A | p.Phe193Leu | missense_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.579C>A | p.Phe193Leu | missense_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-25969C>A | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.901C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
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 | Mar 01, 2023 | The c.579C>A (p.F193L) alteration is located in exon 2 (coding exon 1) of the SPATA13 gene. This alteration results from a C to A substitution at nucleotide position 579, causing the phenylalanine (F) at amino acid position 193 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;N
PrimateAI
Pathogenic
D
Sift4G
Benign
T;T
Vest4
MutPred
Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);
MVP
MPC
ClinPred
D
GERP RS
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
No publications associated with this variant yet.