22-25877941-A-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032608.7(MYO18B):c.4225-18A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: not found (cov: 32)
Consequence
MYO18B
NM_032608.7 intron
NM_032608.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.297
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 3 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 22-25877941-A-C is Benign according to our data. Variant chr22-25877941-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1972670.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO18B | ENST00000335473.12 | c.4225-18A>C | intron_variant | Intron 24 of 43 | 1 | NM_032608.7 | ENSP00000334563.8 | |||
MYO18B | ENST00000407587.6 | c.4228-18A>C | intron_variant | Intron 24 of 43 | 1 | ENSP00000386096.2 | ||||
MYO18B | ENST00000536101.5 | c.4225-18A>C | intron_variant | Intron 24 of 42 | 1 | ENSP00000441229.1 | ||||
MYO18B | ENST00000539302.5 | n.*1683-18A>C | intron_variant | Intron 22 of 41 | 1 | ENSP00000437587.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 16, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.