3-113453506-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144718.4(SPICE1):c.2102G>A(p.Arg701Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,612,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPICE1 | ENST00000295872.8 | c.2102G>A | p.Arg701Gln | missense_variant | Exon 14 of 18 | 1 | NM_144718.4 | ENSP00000295872.4 | ||
ENSG00000285943 | ENST00000649772.1 | n.2102G>A | non_coding_transcript_exon_variant | Exon 14 of 39 | ENSP00000497606.1 | |||||
SPICE1 | ENST00000467618.1 | c.323-5366G>A | intron_variant | Intron 3 of 5 | 5 | ENSP00000420363.1 | ||||
SPICE1 | ENST00000496105.1 | n.1799G>A | non_coding_transcript_exon_variant | Exon 10 of 11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250856Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135512
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460670Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 726392
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2102G>A (p.R701Q) alteration is located in exon 14 (coding exon 13) of the SPICE1 gene. This alteration results from a G to A substitution at nucleotide position 2102, causing the arginine (R) at amino acid position 701 to be replaced by a glutamine (Q). 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