rs2285475
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_002470.4(MYH3):c.3138A>T(p.Arg1046=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,906 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R1046R) has been classified as Benign.
Frequency
Consequence
NM_002470.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH3 | NM_002470.4 | c.3138A>T | p.Arg1046= | synonymous_variant | 25/41 | ENST00000583535.6 | |
MYH3 | XM_011523870.4 | c.3138A>T | p.Arg1046= | synonymous_variant | 25/41 | ||
MYH3 | XM_011523871.3 | c.3138A>T | p.Arg1046= | synonymous_variant | 25/41 | ||
MYH3 | XM_047436127.1 | c.3138A>T | p.Arg1046= | synonymous_variant | 27/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH3 | ENST00000583535.6 | c.3138A>T | p.Arg1046= | synonymous_variant | 25/41 | 5 | NM_002470.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251460Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461872Hom.: 0 Cov.: 65 AF XY: 0.0000303 AC XY: 22AN XY: 727236
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74254
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at