7-120788633-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012338.4(TSPAN12):c.877G>A(p.Ala293Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012338.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPAN12 | NM_012338.4 | c.877G>A | p.Ala293Thr | missense_variant | Exon 8 of 8 | ENST00000222747.8 | NP_036470.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPAN12 | ENST00000222747.8 | c.877G>A | p.Ala293Thr | missense_variant | Exon 8 of 8 | 1 | NM_012338.4 | ENSP00000222747.3 | ||
TSPAN12 | ENST00000415871.5 | c.877G>A | p.Ala293Thr | missense_variant | Exon 9 of 9 | 5 | ENSP00000397699.1 | |||
TSPAN12 | ENST00000450414.5 | n.*727G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 5 | ENSP00000397411.1 | ||||
TSPAN12 | ENST00000450414.5 | n.*727G>A | 3_prime_UTR_variant | Exon 6 of 6 | 5 | ENSP00000397411.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461818Hom.: 0 Cov.: 57 AF XY: 0.00000413 AC XY: 3AN XY: 727206
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1462314). This variant has not been reported in the literature in individuals affected with TSPAN12-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 293 of the TSPAN12 protein (p.Ala293Thr). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at