22-17910798-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015241.3(MICAL3):c.-74-3912G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,184 control chromosomes in the GnomAD database, including 2,727 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 2727 hom., cov: 32)
Consequence
MICAL3
NM_015241.3 intron
NM_015241.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.227
Genes affected
MICAL3 (HGNC:24694): (microtubule associated monooxygenase, calponin and LIM domain containing 3) Enables actin binding activity. Involved in actin filament depolymerization. Located in several cellular components, including Flemming body; intercellular bridge; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICAL3 | NM_015241.3 | c.-74-3912G>A | intron_variant | ENST00000441493.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICAL3 | ENST00000441493.7 | c.-74-3912G>A | intron_variant | 5 | NM_015241.3 | P1 | |||
MICAL3 | ENST00000424046.1 | c.-74-3912G>A | intron_variant | 4 | |||||
MICAL3 | ENST00000495076.5 | c.-74-3912G>A | intron_variant, NMD_transcript_variant | 5 | |||||
MICAL3 | ENST00000672019.1 | c.-74-3912G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28394AN: 152066Hom.: 2727 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.187 AC: 28403AN: 152184Hom.: 2727 Cov.: 32 AF XY: 0.190 AC XY: 14171AN XY: 74420
GnomAD4 genome
?
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AC:
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152184
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32
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14171
AN XY:
74420
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820
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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