6-109444224-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_022765.4(MICAL1):c.3171C>T(p.Ser1057=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,210 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: 33)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
MICAL1
NM_022765.4 synonymous
NM_022765.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.23
Genes affected
MICAL1 (HGNC:20619): (microtubule associated monooxygenase, calponin and LIM domain containing 1) This gene encodes an enzyme that oxidizes methionine residues on actin, thereby promoting depolymerization of actin filaments. This protein interacts with and regulates signalling by NEDD9/CAS-L (neural precursor cell expressed, developmentally down-regulated 9). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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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=-0.66).
BP6
Variant 6-109444224-G-A is Benign according to our data. Variant chr6-109444224-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1941133.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.23 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MICAL1 | NM_022765.4 | c.3171C>T | p.Ser1057= | synonymous_variant | 25/25 | ENST00000358807.8 | NP_073602.3 | |
MICAL1 | NM_001286613.2 | c.3228C>T | p.Ser1076= | synonymous_variant | 25/25 | NP_001273542.1 | ||
MICAL1 | NM_001159291.2 | c.2913C>T | p.Ser971= | synonymous_variant | 24/24 | NP_001152763.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MICAL1 | ENST00000358807.8 | c.3171C>T | p.Ser1057= | synonymous_variant | 25/25 | 1 | NM_022765.4 | ENSP00000351664 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250746Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135790
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461210Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 726888
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GnomAD4 genome Cov.: 33
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Mar 31, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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