16-4783690-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_144605.5(SEPTIN12):c.589G>A(p.Asp197Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Consequence
NM_144605.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN12 | NM_144605.5 | c.589G>A | p.Asp197Asn | missense_variant | 6/10 | ENST00000268231.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN12 | ENST00000268231.13 | c.589G>A | p.Asp197Asn | missense_variant | 6/10 | 1 | NM_144605.5 | P1 | |
SEPTIN12 | ENST00000396693.9 | c.451G>A | p.Asp151Asn | missense_variant | 5/9 | 1 | |||
SEPTIN12 | ENST00000587603.5 | c.589G>A | p.Asp197Asn | missense_variant, NMD_transcript_variant | 6/10 | 2 | |||
SEPTIN12 | ENST00000588241.5 | c.30+2117G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251132Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135804
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461746Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727174
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
Spermatogenic failure 10 Other:2
not provided, no classification provided | literature only | Reproductive Endocrinology and immunology College of Medicine, National Cheng Kung University | - | - - |
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at