2-200472985-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001100423.2(SPATS2L):āc.1214C>Gā(p.Pro405Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,730 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.1214C>G | p.Pro405Arg | missense_variant | 12/13 | ENST00000409140.8 | NP_001093893.1 | |
LOC101927741 | XR_007088047.1 | n.569+3118G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.1214C>G | p.Pro405Arg | missense_variant | 12/13 | 2 | NM_001100423.2 | ENSP00000386730 | P1 | |
ENST00000655656.1 | n.566+3118G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249066Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135142
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461690Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727128
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.1214C>G (p.P405R) alteration is located in exon 12 (coding exon 10) of the SPATS2L gene. This alteration results from a C to G substitution at nucleotide position 1214, causing the proline (P) at amino acid position 405 to be replaced by an arginine (R). 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