4-52062330-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145263.4(SPATA18):c.420C>G(p.Asp140Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000139 in 1,585,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145263.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA18 | NM_145263.4 | c.420C>G | p.Asp140Glu | missense_variant, splice_region_variant | Exon 4 of 13 | ENST00000295213.9 | NP_660306.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151706Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 242308Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130878
GnomAD4 exome AF: 0.00000976 AC: 14AN: 1434158Hom.: 0 Cov.: 26 AF XY: 0.0000140 AC XY: 10AN XY: 714210
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151824Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74160
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.420C>G (p.D140E) alteration is located in exon 4 (coding exon 4) of the SPATA18 gene. This alteration results from a C to G substitution at nucleotide position 420, causing the aspartic acid (D) at amino acid position 140 to be replaced by a glutamic acid (E). 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