11-12305018-G-A

Variant names:

• chr11-12305018-G-A
• rs2172633
• NM_001393937.1:c.5212+10161G>A

Variant summary

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

The NM_001393937.1(MICAL2):​c.5212+10161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,920 control chromosomes in the GnomAD database, including 13,916 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 0.41 (13916 hom., cov: 31)
• Consequence: MICAL2 NM_001393937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 1 publications found

Genes affected

MICAL2 (HGNC:24693): (microtubule associated monooxygenase, calponin and LIM domain containing 2) The protein encoded by this gene is a monooxygenase that enhances depolymerization of F-actin and is therefore involved in cytoskeletal dynamics. The encoded protein is a regulator of the SRF signaling pathway. Increased expression of this gene has been associated with cancer progression and metastasis. [provided by RefSeq, Oct 2016]

ENSG00000254983 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICAL2	NM_001393937.1	c.5212+10161G>A		intron_variant	Intron 31 of 36		NP_001380866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICAL2	ENST00000646065.2	c.5212+10161G>A		intron_variant	Intron 29 of 34			ENSP00000494982.1
ENSG00000254983	ENST00000526616.1	n.268+1218G>A		intron_variant	Intron 1 of 1	3
MICAL2	ENST00000643523.1	n.1717+10161G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62555 AN: 151800 Hom.: 13903 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.412 AC: 62589 AN: 151920 Hom.: 13916 Cov.: 31 AF XY: 0.412 AC XY: 30576 AN XY: 74248

African (AFR) AF: 0.570 AC: 23601 AN: 41402

American (AMR) AF: 0.426 AC: 6511 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2778 AN: 5152

South Asian (SAS) AF: 0.420 AC: 2022 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3373 AN: 10550

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.323 AC: 21962 AN: 67948

Other (OTH) AF: 0.386 AC: 815 AN: 2114

Alfa AF: 0.382 Hom.: 1998

Bravo AF: 0.427

Asia WGS AF: 0.465 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.9
DANN	Benign	0.87
PhyloP100		-0.57

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: rs2172633; hg19: chr11-12326565;