12-109388829-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001101421.4(MYO1H):c.159C>T(p.Ser53Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,611,260 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 5 hom. )
Consequence
MYO1H
NM_001101421.4 synonymous
NM_001101421.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.132
Genes affected
MYO1H (HGNC:13879): (myosin IH) Predicted to enable actin filament binding activity and microfilament motor activity. Predicted to be involved in actin filament organization and vesicle transport along actin filament. Predicted to be part of myosin complex. Predicted to be active in several cellular components, including actin cytoskeleton; microvillus; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1H | NM_001101421.4 | c.159C>T | p.Ser53Ser | synonymous_variant | Exon 2 of 32 | ENST00000310903.10 | NP_001094891.4 | |
MYO1H | XM_011538223.3 | c.111C>T | p.Ser37Ser | synonymous_variant | Exon 3 of 34 | XP_011536525.1 | ||
MYO1H | XM_047428738.1 | c.111C>T | p.Ser37Ser | synonymous_variant | Exon 1 of 31 | XP_047284694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1H | ENST00000310903.10 | c.159C>T | p.Ser53Ser | synonymous_variant | Exon 2 of 32 | 5 | NM_001101421.4 | ENSP00000439182.2 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152030Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000400 AC: 99AN: 247576Hom.: 4 AF XY: 0.000551 AC XY: 74AN XY: 134348
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GnomAD4 exome AF: 0.000217 AC: 316AN: 1459110Hom.: 5 Cov.: 32 AF XY: 0.000329 AC XY: 239AN XY: 725690
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74376
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Not reported inComputational scores
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DS_DG_spliceai
Position offset: -2
DS_DL_spliceai
Position offset: 15
Find out detailed SpliceAI scores and Pangolin per-transcript scores at