17-36498533-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001163735.2(MYO19):āc.2490A>Gā(p.Lys830=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,612,910 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.013 ( 56 hom., cov: 32)
Exomes š: 0.0015 ( 35 hom. )
Consequence
MYO19
NM_001163735.2 synonymous
NM_001163735.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
MYO19 (HGNC:26234): (myosin XIX) Enables actin binding activity. Involved in regulation of cytokinesis and regulation of mitochondrial fission. Acts upstream of or within mitochondrion migration along actin filament. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
ZNHIT3 (HGNC:12309): (zinc finger HIT-type containing 3) Predicted to enable thyroid hormone receptor binding activity. Predicted to be involved in box C/D snoRNP assembly; maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); and snoRNA localization. Located in cytoplasm and nucleus. Implicated in PEHO syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 17-36498533-T-C is Benign according to our data. Variant chr17-36498533-T-C is described in ClinVar as [Benign]. Clinvar id is 785567.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.23 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1983/152362) while in subpopulation AFR AF= 0.0449 (1866/41582). AF 95% confidence interval is 0.0432. There are 56 homozygotes in gnomad4. There are 938 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 56 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO19 | NM_001163735.2 | c.2490A>G | p.Lys830= | synonymous_variant | 25/26 | ENST00000614623.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO19 | ENST00000614623.5 | c.2490A>G | p.Lys830= | synonymous_variant | 25/26 | 2 | NM_001163735.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0130 AC: 1983AN: 152244Hom.: 56 Cov.: 32
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GnomAD3 exomes AF: 0.00368 AC: 916AN: 248682Hom.: 24 AF XY: 0.00285 AC XY: 385AN XY: 134984
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GnomAD4 exome AF: 0.00147 AC: 2143AN: 1460548Hom.: 35 Cov.: 32 AF XY: 0.00134 AC XY: 975AN XY: 726280
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GnomAD4 genome AF: 0.0130 AC: 1983AN: 152362Hom.: 56 Cov.: 32 AF XY: 0.0126 AC XY: 938AN XY: 74518
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 16, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at