Menu
GeneBe

22-17791210-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_015241.3(MICAL3):c.5742G>T(p.Leu1914=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,613,734 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L1914L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0063 ( 9 hom., cov: 33)
Exomes 𝑓: 0.00070 ( 17 hom. )

Consequence

MICAL3
NM_015241.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.15
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 22-17791210-C-A is Benign according to our data. Variant chr22-17791210-C-A is described in ClinVar as [Benign]. Clinvar id is 715940.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.14 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00631 (961/152336) while in subpopulation AFR AF= 0.0214 (889/41582). AF 95% confidence interval is 0.0202. There are 9 homozygotes in gnomad4. There are 469 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MICAL3NM_015241.3 linkuse as main transcriptc.5742G>T p.Leu1914= synonymous_variant 30/32 ENST00000441493.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MICAL3ENST00000441493.7 linkuse as main transcriptc.5742G>T p.Leu1914= synonymous_variant 30/325 NM_015241.3 P1Q7RTP6-1
ENST00000476405.1 linkuse as main transcriptn.981G>T non_coding_transcript_exon_variant 3/52

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00629
AC:
958
AN:
152218
Hom.:
9
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0214
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00909
GnomAD3 exomes
AF:
0.00155
AC:
386
AN:
248468
Hom.:
6
AF XY:
0.00124
AC XY:
167
AN XY:
134908
show subpopulations
Gnomad AFR exome
AF:
0.0195
Gnomad AMR exome
AF:
0.00131
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000197
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000204
Gnomad OTH exome
AF:
0.00165
GnomAD4 exome
AF:
0.000698
AC:
1020
AN:
1461398
Hom.:
17
Cov.:
32
AF XY:
0.000616
AC XY:
448
AN XY:
726964
show subpopulations
Gnomad4 AFR exome
AF:
0.0206
Gnomad4 AMR exome
AF:
0.00145
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000120
Gnomad4 OTH exome
AF:
0.00154
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00631
AC:
961
AN:
152336
Hom.:
9
Cov.:
33
AF XY:
0.00630
AC XY:
469
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.0214
Gnomad4 AMR
AF:
0.00255
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00900
Alfa
AF:
0.00319
Hom.:
2
Bravo
AF:
0.00705
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.24
Cadd
Benign
14
Dann
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs115182420; hg19: chr22-18273976; API