1-153537419-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394232.1(S100A5):āc.156C>Gā(p.Ile52Met) 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 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_001394232.1 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 | UniProt |
---|---|---|---|---|---|---|---|
S100A5 | NM_001394232.1 | c.156C>G | p.Ile52Met | missense_variant | 3/3 | ENST00000368717.3 | |
LOC124904423 | XR_007066630.1 | n.2996G>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S100A5 | ENST00000368717.3 | c.156C>G | p.Ile52Met | missense_variant | 3/3 | 3 | NM_001394232.1 | P1 | |
S100A5 | ENST00000368718.5 | c.156C>G | p.Ile52Met | missense_variant | 4/4 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250920Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135674
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727212
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.156C>G (p.I52M) alteration is located in exon 4 (coding exon 2) of the S100A5 gene. This alteration results from a C to G substitution at nucleotide position 156, causing the isoleucine (I) at amino acid position 52 to be replaced by a methionine (M). 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