17-32995574-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173847.5(SPACA3):āc.200C>Gā(p.Ala67Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,894 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_173847.5 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPACA3 | NM_173847.5 | c.200C>G | p.Ala67Gly | missense_variant | 2/5 | ENST00000269053.8 | NP_776246.1 | |
SPACA3 | NM_001317225.2 | c.-99C>G | 5_prime_UTR_variant | 2/5 | NP_001304154.1 | |||
SPACA3 | NM_001317226.2 | c.35-1269C>G | intron_variant | NP_001304155.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPACA3 | ENST00000269053.8 | c.200C>G | p.Ala67Gly | missense_variant | 2/5 | 1 | NM_173847.5 | ENSP00000269053.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251360Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135862
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2024 | The c.200C>G (p.A67G) alteration is located in exon 2 (coding exon 2) of the SPACA3 gene. This alteration results from a C to G substitution at nucleotide position 200, causing the alanine (A) at amino acid position 67 to be replaced by a glycine (G). 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