rs150370442
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_145207.3(SPATA5):c.830A>T(p.Asp277Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000582 in 1,614,106 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_145207.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5 | NM_145207.3 | c.830A>T | p.Asp277Val | missense_variant | 5/16 | ENST00000274008.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2A | ENST00000274008.5 | c.830A>T | p.Asp277Val | missense_variant | 5/16 | 1 | NM_145207.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000407 AC: 62AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000346 AC: 87AN: 251358Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135862
GnomAD4 exome AF: 0.000600 AC: 877AN: 1461890Hom.: 2 Cov.: 31 AF XY: 0.000600 AC XY: 436AN XY: 727248
GnomAD4 genome ? AF: 0.000407 AC: 62AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000350 AC XY: 26AN XY: 74358
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.830A>T (p.D277V) alteration is located in exon 5 (coding exon 5) of the SPATA5 gene. This alteration results from a A to T substitution at nucleotide position 830, causing the aspartic acid (D) at amino acid position 277 to be replaced by a valine (V). The p.D277V alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 25, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at