rs5992105

Variant names:

• chr22-17800481-A-G
• rs5992105
• NM_015241.3:c.5650+8363T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015241.3(MICAL3):​c.5650+8363T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,112 control chromosomes in the GnomAD database, including 5,090 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 (5090 hom., cov: 32)
• Consequence: MICAL3 NM_015241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 7 publications found

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]

ENSG00000093100 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015241.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICAL3	NM_015241.3	MANE Select	c.5650+8363T>C		intron	N/A	NP_056056.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICAL3	ENST00000441493.7	TSL:5 MANE Select	c.5650+8363T>C		intron	N/A	ENSP00000416015.2
	MICAL3	ENST00000577821.5	TSL:3	c.580+3330T>C		intron	N/A	ENSP00000463882.1
	MICAL3	ENST00000579997.5	TSL:5	c.416-6687T>C		intron	N/A	ENSP00000462107.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28187 AN: 151994 Hom.: 5061 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.156

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.186 AC: 28266 AN: 152112 Hom.: 5090 Cov.: 32 AF XY: 0.183 AC XY: 13611 AN XY: 74370

African (AFR) AF: 0.473 AC: 19584 AN: 41432

American (AMR) AF: 0.0793 AC: 1213 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.167 AC: 864 AN: 5172

South Asian (SAS) AF: 0.155 AC: 746 AN: 4822

European-Finnish (FIN) AF: 0.0537 AC: 570 AN: 10610

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0662 AC: 4504 AN: 67996

Other (OTH) AF: 0.156 AC: 330 AN: 2116

Alfa AF: 0.0968 Hom.: 2254

Bravo AF: 0.198

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.85
PhyloP100		0.089
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5992105; hg19: chr22-18283247;