3-172924227-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_031955.6(SPATA16):c.1319T>C(p.Ile440Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000409 in 1,613,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I440M) has been classified as Uncertain significance.
Frequency
Consequence
NM_031955.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA16 | NM_031955.6 | c.1319T>C | p.Ile440Thr | missense_variant | 8/11 | ENST00000351008.4 | |
SPATA16 | XM_006713778.4 | c.1319T>C | p.Ile440Thr | missense_variant | 8/11 | ||
SPATA16 | XM_017007308.3 | c.1319T>C | p.Ile440Thr | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA16 | ENST00000351008.4 | c.1319T>C | p.Ile440Thr | missense_variant | 8/11 | 1 | NM_031955.6 | P1 | |
SPATA16 | ENST00000652082.1 | c.473T>C | p.Ile158Thr | missense_variant, NMD_transcript_variant | 4/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251030Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135694
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1460828Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726758
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.1319T>C (p.I440T) alteration is located in exon 8 (coding exon 7) of the SPATA16 gene. This alteration results from a T to C substitution at nucleotide position 1319, causing the isoleucine (I) at amino acid position 440 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at