13-24223031-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001166271.3(SPATA13):c.102G>A(p.Ser34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,551,640 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00067 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00019 ( 2 hom. )
Consequence
SPATA13
NM_001166271.3 synonymous
NM_001166271.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
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 Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 13-24223031-G-A is Benign according to our data. Variant chr13-24223031-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041432.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
BS2
?
High AC in GnomAd at 102 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.102G>A | p.Ser34= | synonymous_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.288G>A | p.Ser96= | synonymous_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26446G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.102G>A | p.Ser34= | synonymous_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.102G>A | p.Ser34= | synonymous_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-26446G>A | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.424G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000670 AC: 102AN: 152190Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000426 AC: 66AN: 155082Hom.: 0 AF XY: 0.000523 AC XY: 43AN XY: 82258
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GnomAD4 exome AF: 0.000192 AC: 269AN: 1399332Hom.: 2 Cov.: 29 AF XY: 0.000217 AC XY: 150AN XY: 690168
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SPATA13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at