chr5-79729249-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153610.5(CMYA5):c.484C>T(p.Pro162Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,458,296 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 (★).
Frequency
Consequence
NM_153610.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.484C>T | p.Pro162Ser | missense_variant | 2/13 | ENST00000446378.3 | NP_705838.3 | |
CMYA5 | XM_047416911.1 | c.484C>T | p.Pro162Ser | missense_variant | 2/6 | XP_047272867.1 | ||
CMYA5 | XR_001742036.3 | n.556C>T | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CMYA5 | ENST00000446378.3 | c.484C>T | p.Pro162Ser | missense_variant | 2/13 | 5 | NM_153610.5 | ENSP00000394770 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245376Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133122
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458296Hom.: 0 Cov.: 34 AF XY: 0.00000414 AC XY: 3AN XY: 725414
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 23, 2024 | The c.484C>T (p.P162S) alteration is located in exon 2 (coding exon 2) of the CMYA5 gene. This alteration results from a C to T substitution at nucleotide position 484, causing the proline (P) at amino acid position 162 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