chr11-2302943-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139022.3(TSPAN32):āc.166G>Cā(p.Ala56Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,446 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_139022.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPAN32 | NM_139022.3 | c.166G>C | p.Ala56Pro | missense_variant | 2/10 | ENST00000182290.9 | NP_620591.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPAN32 | ENST00000182290.9 | c.166G>C | p.Ala56Pro | missense_variant | 2/10 | 1 | NM_139022.3 | ENSP00000182290.5 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250240Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135402
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461212Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726912
GnomAD4 genome AF: 0.000131 AC: 20AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2024 | The c.166G>C (p.A56P) alteration is located in exon 2 (coding exon 2) of the TSPAN32 gene. This alteration results from a G to C substitution at nucleotide position 166, causing the alanine (A) at amino acid position 56 to be replaced by a proline (P). 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