5-79729172-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153610.5(CMYA5):c.407A>T(p.His136Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.407A>T | p.His136Leu | missense_variant | 2/13 | ENST00000446378.3 | NP_705838.3 | |
CMYA5 | XM_047416911.1 | c.407A>T | p.His136Leu | missense_variant | 2/6 | XP_047272867.1 | ||
CMYA5 | XR_001742036.3 | n.479A>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.407A>T | p.His136Leu | missense_variant | 2/13 | 5 | NM_153610.5 | ENSP00000394770 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247906Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134426
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460510Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726432
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.407A>T (p.H136L) alteration is located in exon 2 (coding exon 2) of the CMYA5 gene. This alteration results from a A to T substitution at nucleotide position 407, causing the histidine (H) at amino acid position 136 to be replaced by a leucine (L). 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