12-49496911-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023071.4(SPATS2):c.605C>G(p.Pro202Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,288 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023071.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATS2 | NM_023071.4 | c.605C>G | p.Pro202Arg | missense_variant | Exon 8 of 14 | ENST00000552918.6 | NP_075559.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250354Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135344
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461030Hom.: 1 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 726824
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.605C>G (p.P202R) alteration is located in exon 8 (coding exon 6) of the SPATS2 gene. This alteration results from a C to G substitution at nucleotide position 605, causing the proline (P) at amino acid position 202 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