13-112399091-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145248.5(SPACA7):āc.267A>Cā(p.Gln89His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,609,546 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 (ā ).
Frequency
Consequence
NM_145248.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPACA7 | NM_145248.5 | c.267A>C | p.Gln89His | missense_variant | 4/7 | ENST00000283550.8 | |
LOC105370372 | XR_944294.2 | n.330-7697T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPACA7 | ENST00000283550.8 | c.267A>C | p.Gln89His | missense_variant | 4/7 | 1 | NM_145248.5 | P1 | |
SPACA7 | ENST00000375699.3 | c.174A>C | p.Gln58His | missense_variant | 3/6 | 3 | |||
SPACA7 | ENST00000443541.5 | c.225A>C | p.Gln75His | missense_variant | 5/6 | 3 | |||
SPACA7 | ENST00000414180.5 | c.231A>C | p.Gln77His | missense_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250090Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135102
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1457316Hom.: 0 Cov.: 28 AF XY: 0.00000689 AC XY: 5AN XY: 725186
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.267A>C (p.Q89H) alteration is located in exon 4 (coding exon 4) of the SPACA7 gene. This alteration results from a A to C substitution at nucleotide position 267, causing the glutamine (Q) at amino acid position 89 to be replaced by a histidine (H). 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