17-32995453-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001317225.2(SPACA3):c.-220C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,496 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_001317225.2 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
SPACA3 | NM_173847.5 | c.79C>T | p.Arg27Trp | missense_variant | Exon 2 of 5 | ENST00000269053.8 | NP_776246.1 | |
SPACA3 | NM_001317225.2 | c.-220C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | NP_001304154.1 | |||
SPACA3 | NM_001317225.2 | c.-220C>T | 5_prime_UTR_variant | Exon 2 of 5 | NP_001304154.1 | |||
SPACA3 | NM_001317226.2 | c.35-1390C>T | intron_variant | Intron 1 of 3 | NP_001304155.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248606Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134464
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1460352Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726222
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.79C>T (p.R27W) alteration is located in exon 2 (coding exon 2) of the SPACA3 gene. This alteration results from a C to T substitution at nucleotide position 79, causing the arginine (R) at amino acid position 27 to be replaced by a tryptophan (W). 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