Genetic Variant MICAL3:c.5445+929C>A (chr22-17815761-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015241.3(MICAL3):c.5445+929C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,236 control chromosomes in the GnomAD database, including 7,294 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 0.30 ( 7289 hom., cov: 33)

Exomes 𝑓: 0.29 ( 5 hom. )

Consequence

MICAL3
NM_015241.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

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]

MICAL3 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICAL3	NM_015241.3 link	c.5445+929C>A		intron_variant	Intron 27 of 31	ENST00000441493.7	NP_056056.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICAL3	ENST00000441493.7 link	c.5445+929C>A		intron_variant	Intron 27 of 31	5	NM_015241.3	ENSP00000416015.2		Q7RTP6-1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45924

AN:

151982

Hom.:

7288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.292

GnomAD4 exome

AF:

0.287

AC:

AN:

136

Hom.:

AF XY:

0.255

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.389

Gnomad4 NFE exome

AF:

0.281

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.302

AC:

45939

AN:

152100

Hom.:

7289

Cov.:

AF XY:

0.299

AC XY:

22242

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.273

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.402

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.325

Hom.:

4119

Bravo

AF:

0.292

Asia WGS

AF:

0.162

AC:

563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over