chr15-71827917-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_006901.4(MYO9A):āc.7150A>Gā(p.Met2384Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006901.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO9A | NM_006901.4 | c.7150A>G | p.Met2384Val | missense_variant | 41/42 | ENST00000356056.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO9A | ENST00000356056.10 | c.7150A>G | p.Met2384Val | missense_variant | 41/42 | 1 | NM_006901.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000598 AC: 91AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 250984Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135644
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461484Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 727042
GnomAD4 genome AF: 0.000597 AC: 91AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74482
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2021 | The c.7150A>G (p.M2384V) alteration is located in exon 41 (coding exon 40) of the MYO9A gene. This alteration results from a A to G substitution at nucleotide position 7150, causing the methionine (M) at amino acid position 2384 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at