chr1-153547821-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002960.2(S100A3):c.167A>G(p.Asn56Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002960.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
S100A3 | NM_002960.2 | c.167A>G | p.Asn56Ser | missense_variant | 3/3 | ENST00000368713.8 | |
LOC101928034 | NR_125947.1 | n.169-600T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S100A3 | ENST00000368713.8 | c.167A>G | p.Asn56Ser | missense_variant | 3/3 | 1 | NM_002960.2 | P1 | |
S100A3 | ENST00000368712.1 | c.167A>G | p.Asn56Ser | missense_variant | 3/3 | 3 | P1 | ||
S100A4 | ENST00000368714.1 | c.-16+2244A>G | intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251300Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135800
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000825 AC XY: 60AN XY: 727178
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.167A>G (p.N56S) alteration is located in exon 3 (coding exon 2) of the S100A3 gene. This alteration results from a A to G substitution at nucleotide position 167, causing the asparagine (N) at amino acid position 56 to be replaced by a serine (S). 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