chr17-29086536-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_078471.4(MYO18A):c.5754G>T(p.Leu1918=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,613,072 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0039 ( 23 hom. )
Consequence
MYO18A
NM_078471.4 synonymous
NM_078471.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.275
Genes affected
MYO18A (HGNC:31104): (myosin XVIIIA) The protein encoded by this gene can bind GOLPH3, linking the Golgi to the cytoskeleton and influencing Golgi membrane trafficking. The encoded protein is also part of a complex that assembles lamellar actomyosin bundles and may be required for cell migration. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
BP6
?
Variant 17-29086536-C-A is Benign according to our data. Variant chr17-29086536-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2647607.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.275 with no splicing effect.
BS2
?
High AC in GnomAd at 317 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO18A | NM_078471.4 | c.5754G>T | p.Leu1918= | synonymous_variant | 39/42 | ENST00000527372.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO18A | ENST00000527372.7 | c.5754G>T | p.Leu1918= | synonymous_variant | 39/42 | 1 | NM_078471.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00208 AC: 317AN: 152210Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00163 AC: 402AN: 246860Hom.: 0 AF XY: 0.00163 AC XY: 218AN XY: 134014
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GnomAD4 exome AF: 0.00387 AC: 5656AN: 1460744Hom.: 23 Cov.: 33 AF XY: 0.00365 AC XY: 2653AN XY: 726552
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GnomAD4 genome ? AF: 0.00208 AC: 317AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.00168 AC XY: 125AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | MYO18A: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at