6-88048003-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_030960.3(SPACA1):c.98C>T(p.Thr33Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,585,156 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030960.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPACA1 | NM_030960.3 | c.98C>T | p.Thr33Ile | missense_variant | Exon 1 of 7 | ENST00000237201.2 | NP_112222.1 | |
SPACA1 | XM_047419385.1 | c.98C>T | p.Thr33Ile | missense_variant | Exon 1 of 6 | XP_047275341.1 | ||
SPACA1 | XM_011536160.3 | c.-39+818C>T | intron_variant | Intron 1 of 6 | XP_011534462.1 | |||
SPACA1 | XM_017011335.2 | c.-39+822C>T | intron_variant | Intron 1 of 6 | XP_016866824.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000807 AC: 16AN: 198164Hom.: 0 AF XY: 0.0000749 AC XY: 8AN XY: 106850
GnomAD4 exome AF: 0.000107 AC: 154AN: 1432828Hom.: 2 Cov.: 31 AF XY: 0.000114 AC XY: 81AN XY: 709580
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.98C>T (p.T33I) alteration is located in exon 1 (coding exon 1) of the SPACA1 gene. This alteration results from a C to T substitution at nucleotide position 98, causing the threonine (T) at amino acid position 33 to be replaced by an isoleucine (I). 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