rs143957561
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145207.3(SPATA5):c.1622C>A(p.Pro541His) variant causes a missense change. The variant allele was found at a frequency of 0.0000103 in 1,461,858 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P541R) has been classified as Likely benign.
Frequency
Consequence
NM_145207.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5 | NM_145207.3 | c.1622C>A | p.Pro541His | missense_variant | 9/16 | ENST00000274008.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2A | ENST00000274008.5 | c.1622C>A | p.Pro541His | missense_variant | 9/16 | 1 | NM_145207.3 | P1 | |
AFG2A | ENST00000422835.2 | n.1664C>A | non_coding_transcript_exon_variant | 9/15 | 1 | ||||
AFG2A | ENST00000675612.1 | c.1619C>A | p.Pro540His | missense_variant | 9/17 | ||||
AFG2A | ENST00000674886.1 | n.1684C>A | non_coding_transcript_exon_variant | 9/11 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251432Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135884
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at