chr5-79729078-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_153610.5(CMYA5):c.313G>C(p.Gly105Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000339 in 1,613,900 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G105G) has been classified as Likely benign.
Frequency
Consequence
NM_153610.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.313G>C | p.Gly105Arg | missense_variant | 2/13 | ENST00000446378.3 | |
CMYA5 | XM_047416911.1 | c.313G>C | p.Gly105Arg | missense_variant | 2/6 | ||
CMYA5 | XR_001742036.3 | n.385G>C | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMYA5 | ENST00000446378.3 | c.313G>C | p.Gly105Arg | missense_variant | 2/13 | 5 | NM_153610.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00169 AC: 257AN: 152106Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000530 AC: 132AN: 249126Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135152
GnomAD4 exome AF: 0.000198 AC: 289AN: 1461676Hom.: 1 Cov.: 33 AF XY: 0.000173 AC XY: 126AN XY: 727120
GnomAD4 genome ? AF: 0.00169 AC: 258AN: 152224Hom.: 1 Cov.: 32 AF XY: 0.00176 AC XY: 131AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at