17-75589548-A-G
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001395058.1(MYO15B):āc.1491A>Gā(p.Leu497Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 398,590 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 (ā ).
Frequency
Genomes: š 0.00061 ( 0 hom., cov: 32)
Exomes š: 0.00084 ( 0 hom. )
Consequence
MYO15B
NM_001395058.1 synonymous
NM_001395058.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.20
Genes affected
MYO15B (HGNC:14083): (myosin XVB) Predicted to enable ATP binding activity; actin binding activity; and cytoskeletal motor activity. Predicted to be located in brush border; cytoplasm; and cytoskeleton. Predicted to be part of myosin complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 17-75589548-A-G is Benign according to our data. Variant chr17-75589548-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648266.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.2 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO15B | NM_001395058.1 | c.1491A>G | p.Leu497Leu | synonymous_variant | Exon 1 of 64 | ENST00000645453.3 | NP_001381987.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO15B | ENST00000645453.3 | c.1491A>G | p.Leu497Leu | synonymous_variant | Exon 1 of 64 | NM_001395058.1 | ENSP00000495242.3 |
Frequencies
GnomAD3 genomes AF: 0.000606 AC: 92AN: 151928Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000844 AC: 208AN: 246544Hom.: 0 Cov.: 0 AF XY: 0.000904 AC XY: 113AN XY: 125016
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GnomAD4 genome AF: 0.000605 AC: 92AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.000592 AC XY: 44AN XY: 74326
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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
May 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
MYO15B: BP4, BP7 -
Computational scores
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Benign
CADD
Benign
DANN
Benign
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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