chr22-25763216-G-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032608.7(MYO18B):c.40-15G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
MYO18B
NM_032608.7 splice_polypyrimidine_tract, intron
NM_032608.7 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0830
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
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 22-25763216-G-C is Benign according to our data. Variant chr22-25763216-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3011070.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO18B | NM_032608.7 | c.40-15G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000335473.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO18B | ENST00000335473.12 | c.40-15G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032608.7 | A2 | |||
MYO18B | ENST00000407587.6 | c.40-15G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | P5 | ||||
MYO18B | ENST00000536101.5 | c.40-15G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
MYO18B | ENST00000539302.5 | c.40-15G>C | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455954Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 723364
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30
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Bravo
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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 | Invitae | Feb 13, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at