chr22-25761113-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_032608.7(MYO18B):c.21C>T(p.Leu7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,374 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000057 ( 1 hom. )
Consequence
MYO18B
NM_032608.7 synonymous
NM_032608.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.893
Genes affected
MYO18B (HGNC:18150): (myosin XVIIIB) The protein encoded by this gene may regulate muscle-specific genes when in the nucleus and may influence intracellular trafficking when in the cytoplasm. The encoded protein functions as a homodimer and may interact with F actin. Mutations in this gene are associated with lung cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
Variant 22-25761113-C-T is Benign according to our data. Variant chr22-25761113-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1673380.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.893 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO18B | NM_032608.7 | c.21C>T | p.Leu7= | synonymous_variant | 2/44 | ENST00000335473.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO18B | ENST00000335473.12 | c.21C>T | p.Leu7= | synonymous_variant | 2/44 | 1 | NM_032608.7 | A2 | |
MYO18B | ENST00000407587.6 | c.21C>T | p.Leu7= | synonymous_variant | 2/44 | 1 | P5 | ||
MYO18B | ENST00000536101.5 | c.21C>T | p.Leu7= | synonymous_variant | 2/43 | 1 | A2 | ||
MYO18B | ENST00000539302.5 | c.21C>T | p.Leu7= | synonymous_variant, NMD_transcript_variant | 1/42 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248924Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135026
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GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461176Hom.: 1 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 726914
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
MYO18B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 07, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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