1-153540157-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001394232.1(S100A5):c.35T>C(p.Met12Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394232.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
S100A5 | NM_001394232.1 | c.35T>C | p.Met12Thr | missense_variant | Exon 2 of 3 | ENST00000368717.3 | NP_001381161.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
S100A5 | ENST00000368717.3 | c.35T>C | p.Met12Thr | missense_variant | Exon 2 of 3 | 3 | NM_001394232.1 | ENSP00000357706.2 | ||
S100A5 | ENST00000368718.5 | c.35T>C | p.Met12Thr | missense_variant | Exon 3 of 4 | 1 | ENSP00000357707.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251492Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727240
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.35T>C (p.M12T) alteration is located in exon 3 (coding exon 1) of the S100A5 gene. This alteration results from a T to C substitution at nucleotide position 35, causing the methionine (M) at amino acid position 12 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