rs751925881
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_145207.3(SPATA5):c.1209C>T(p.Ile403=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,714 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 1 hom. )
Consequence
SPATA5
NM_145207.3 synonymous
NM_145207.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
AFG2A (HGNC:18119): (AFG2 AAA ATPase homolog A) This gene encodes a member of the ATPase associated with diverse activities family, whose members are defined by a highly conserved ATPase domain. Members of this family participate in diverse cellular processes that include membrane fusion, DNA replication, microtubule severing, and protein degradation. The protein encoded by this gene has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Allelic variants in this gene have been associated with epilepsy, hearing loss, and cognitive disability syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 4-122935775-C-T is Benign according to our data. Variant chr4-122935775-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 475717.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.28 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5 | NM_145207.3 | c.1209C>T | p.Ile403= | synonymous_variant | 6/16 | ENST00000274008.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2A | ENST00000274008.5 | c.1209C>T | p.Ile403= | synonymous_variant | 6/16 | 1 | NM_145207.3 | P1 | |
AFG2A | ENST00000422835.2 | n.1251C>T | non_coding_transcript_exon_variant | 6/15 | 1 | ||||
AFG2A | ENST00000675612.1 | c.1206C>T | p.Ile402= | synonymous_variant | 6/17 | ||||
AFG2A | ENST00000674886.1 | n.1271C>T | non_coding_transcript_exon_variant | 6/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152102Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251094Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135714
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GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460612Hom.: 1 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726572
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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