chr3-172924226-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031955.6(SPATA16):c.1320T>G(p.Ile440Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,612,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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. I440T) has been classified as Uncertain significance.
Frequency
Consequence
NM_031955.6 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 |
---|---|---|---|---|---|---|---|
SPATA16 | NM_031955.6 | c.1320T>G | p.Ile440Met | missense_variant | 8/11 | ENST00000351008.4 | |
SPATA16 | XM_006713778.4 | c.1320T>G | p.Ile440Met | missense_variant | 8/11 | ||
SPATA16 | XM_017007308.3 | c.1320T>G | p.Ile440Met | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA16 | ENST00000351008.4 | c.1320T>G | p.Ile440Met | missense_variant | 8/11 | 1 | NM_031955.6 | P1 | |
SPATA16 | ENST00000652082.1 | c.474T>G | p.Ile158Met | missense_variant, NMD_transcript_variant | 4/8 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 251034Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135694
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1460624Hom.: 0 Cov.: 30 AF XY: 0.0000440 AC XY: 32AN XY: 726686
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.1320T>G (p.I440M) alteration is located in exon 8 (coding exon 7) of the SPATA16 gene. This alteration results from a T to G substitution at nucleotide position 1320, causing the isoleucine (I) at amino acid position 440 to be replaced by a methionine (M). 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