chr12-57746249-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000257910.8(TSPAN31):āc.305G>Cā(p.Ser102Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000257910.8 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 |
---|---|---|---|---|---|---|---|---|
TSPAN31 | NM_005981.5 | c.305G>C | p.Ser102Thr | missense_variant | 3/6 | ENST00000257910.8 | NP_005972.1 | |
TSPAN31 | NM_001330169.2 | c.71G>C | p.Ser24Thr | missense_variant | 3/6 | NP_001317098.1 | ||
TSPAN31 | XM_024449123.2 | c.71G>C | p.Ser24Thr | missense_variant | 3/6 | XP_024304891.1 | ||
TSPAN31 | NM_001330168.2 | c.64-340G>C | intron_variant | NP_001317097.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPAN31 | ENST00000257910.8 | c.305G>C | p.Ser102Thr | missense_variant | 3/6 | 1 | NM_005981.5 | ENSP00000257910 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251468Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135914
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461546Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727100
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.305G>C (p.S102T) alteration is located in exon 3 (coding exon 3) of the TSPAN31 gene. This alteration results from a G to C substitution at nucleotide position 305, causing the serine (S) at amino acid position 102 to be replaced by a threonine (T). 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