chr3-113446669-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_144718.4(SPICE1):c.2434G>A(p.Gly812Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,612,002 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144718.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPICE1 | ENST00000295872.8 | c.2434G>A | p.Gly812Arg | missense_variant | Exon 17 of 18 | 1 | NM_144718.4 | ENSP00000295872.4 | ||
ENSG00000285943 | ENST00000649772.1 | n.2434G>A | non_coding_transcript_exon_variant | Exon 17 of 39 | ENSP00000497606.1 | |||||
SPICE1 | ENST00000467618.1 | c.433G>A | p.Gly145Arg | missense_variant | Exon 5 of 6 | 5 | ENSP00000420363.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000204 AC: 51AN: 249544Hom.: 0 AF XY: 0.000171 AC XY: 23AN XY: 134734
GnomAD4 exome AF: 0.000142 AC: 208AN: 1459946Hom.: 0 Cov.: 29 AF XY: 0.000153 AC XY: 111AN XY: 726234
GnomAD4 genome AF: 0.000105 AC: 16AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2434G>A (p.G812R) alteration is located in exon 17 (coding exon 16) of the SPICE1 gene. This alteration results from a G to A substitution at nucleotide position 2434, causing the glycine (G) at amino acid position 812 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