X-56994916-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001010862.3(SPIN3):c.32G>A(p.Gly11Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,196,715 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010862.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPIN3 | ENST00000374919.6 | c.32G>A | p.Gly11Glu | missense_variant | Exon 2 of 2 | 1 | NM_001010862.3 | ENSP00000364054.3 | ||
SPIN3 | ENST00000639257.1 | n.32G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 3 | ENSP00000492259.1 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112084Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34274
GnomAD3 exomes AF: 0.0000121 AC: 2AN: 165643Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 54533
GnomAD4 exome AF: 0.0000101 AC: 11AN: 1084631Hom.: 0 Cov.: 31 AF XY: 0.0000113 AC XY: 4AN XY: 352483
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112084Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.32G>A (p.G11E) alteration is located in exon 2 (coding exon 1) of the SPIN3 gene. This alteration results from a G to A substitution at nucleotide position 32, causing the glycine (G) at amino acid position 11 to be replaced by a glutamic acid (E). 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