9-70298090-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015110.4(SMC5):c.1178G>A(p.Cys393Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. C393C) has been classified as Likely benign.
Frequency
Consequence
NM_015110.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC5 | NM_015110.4 | c.1178G>A | p.Cys393Tyr | missense_variant | 9/25 | ENST00000361138.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC5 | ENST00000361138.7 | c.1178G>A | p.Cys393Tyr | missense_variant | 9/25 | 1 | NM_015110.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251246Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135772
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 727184
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at