3-108394093-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014981.3(MYH15):c.5197G>A(p.Ala1733Thr) 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 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014981.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH15 | NM_014981.3 | c.5197G>A | p.Ala1733Thr | missense_variant | 36/41 | ENST00000693548.1 | |
MYH15 | XM_011512559.3 | c.5257G>A | p.Ala1753Thr | missense_variant | 38/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH15 | ENST00000693548.1 | c.5197G>A | p.Ala1733Thr | missense_variant | 36/41 | NM_014981.3 | P1 | ||
MYH15 | ENST00000273353.5 | c.5197G>A | p.Ala1733Thr | missense_variant | 37/42 | 1 | P1 | ||
MYH15 | ENST00000689784.1 | c.4216G>A | p.Ala1406Thr | missense_variant | 28/33 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249178Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135160
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727202
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.5257G>A (p.A1753T) alteration is located in exon 37 (coding exon 37) of the MYH15 gene. This alteration results from a G to A substitution at nucleotide position 5257, causing the alanine (A) at amino acid position 1753 to be replaced by a threonine (T). 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