5-79729183-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153610.5(CMYA5):āc.418C>Gā(p.His140Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_153610.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.418C>G | p.His140Asp | missense_variant | 2/13 | ENST00000446378.3 | NP_705838.3 | |
CMYA5 | XM_047416911.1 | c.418C>G | p.His140Asp | missense_variant | 2/6 | XP_047272867.1 | ||
CMYA5 | XR_001742036.3 | n.490C>G | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CMYA5 | ENST00000446378.3 | c.418C>G | p.His140Asp | missense_variant | 2/13 | 5 | NM_153610.5 | ENSP00000394770 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 247998Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134516
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460714Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 726610
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.418C>G (p.H140D) alteration is located in exon 2 (coding exon 2) of the CMYA5 gene. This alteration results from a C to G substitution at nucleotide position 418, causing the histidine (H) at amino acid position 140 to be replaced by an aspartic acid (D). 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