rs767423681
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_145207.3(SPATA5):c.1365G>A(p.Leu455=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000528 in 1,608,980 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L455L) has been classified as Likely benign.
Frequency
Consequence
NM_145207.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5 | NM_145207.3 | c.1365G>A | p.Leu455= | synonymous_variant | 8/16 | ENST00000274008.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2A | ENST00000274008.5 | c.1365G>A | p.Leu455= | synonymous_variant | 8/16 | 1 | NM_145207.3 | P1 | |
AFG2A | ENST00000422835.2 | n.1407G>A | non_coding_transcript_exon_variant | 8/15 | 1 | ||||
AFG2A | ENST00000675612.1 | c.1362G>A | p.Leu454= | synonymous_variant | 8/17 | ||||
AFG2A | ENST00000674886.1 | n.1427G>A | non_coding_transcript_exon_variant | 8/11 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248412Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134230
GnomAD4 exome AF: 0.0000522 AC: 76AN: 1456884Hom.: 0 Cov.: 30 AF XY: 0.0000469 AC XY: 34AN XY: 724504
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | AFG2A: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 27, 2021 | - - |
Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at