2-200439194-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001100423.2(SPATS2L):āc.518G>Cā(p.Arg173Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001100423.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.518G>C | p.Arg173Thr | missense_variant | 7/13 | ENST00000409140.8 | NP_001093893.1 | |
LOC101927741 | XR_007088047.1 | n.663-7657C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.518G>C | p.Arg173Thr | missense_variant | 7/13 | 2 | NM_001100423.2 | ENSP00000386730 | P1 | |
ENST00000655656.1 | n.567-7657C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248816Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134950
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461474Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727012
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2023 | The c.518G>C (p.R173T) alteration is located in exon 7 (coding exon 5) of the SPATS2L gene. This alteration results from a G to C substitution at nucleotide position 518, causing the arginine (R) at amino acid position 173 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