1-153563870-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005978.4(S100A2):āc.8G>Cā(p.Cys3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00204 in 1,613,900 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005978.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
S100A2 | NM_005978.4 | c.8G>C | p.Cys3Ser | missense_variant | 2/3 | ENST00000368708.9 | |
S100A2 | NM_001366406.1 | c.8G>C | p.Cys3Ser | missense_variant | 1/3 | ||
S100A2 | XM_047427373.1 | c.8G>C | p.Cys3Ser | missense_variant | 2/4 | ||
S100A2 | NM_001366407.1 | c.-78-17G>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S100A2 | ENST00000368708.9 | c.8G>C | p.Cys3Ser | missense_variant | 2/3 | 1 | NM_005978.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 576AN: 152190Hom.: 16 Cov.: 31
GnomAD3 exomes AF: 0.00803 AC: 2015AN: 250888Hom.: 69 AF XY: 0.00632 AC XY: 857AN XY: 135590
GnomAD4 exome AF: 0.00185 AC: 2708AN: 1461592Hom.: 82 Cov.: 33 AF XY: 0.00162 AC XY: 1181AN XY: 727094
GnomAD4 genome ? AF: 0.00380 AC: 579AN: 152308Hom.: 17 Cov.: 31 AF XY: 0.00407 AC XY: 303AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at