chr11-12127984-C-T

Variant names:

• chr11-12127984-C-T
• rs2013486
• NM_001282663.2:c.-148-10406C>T

Variant summary

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

The NM_001282663.2(MICAL2):​c.-148-10406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,200 control chromosomes in the GnomAD database, including 3,050 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 0.18 (3050 hom., cov: 33)
• Consequence: MICAL2 NM_001282663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICAL2	NM_001282663.2	c.-148-10406C>T		intron_variant	Intron 1 of 27	ENST00000683283.1	NP_001269592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICAL2	ENST00000683283.1	c.-148-10406C>T		intron_variant	Intron 1 of 27		NM_001282663.2	ENSP00000507067.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28119 AN: 152082 Hom.: 3047 Cov.: 33

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.185 AC: 28133 AN: 152200 Hom.: 3050 Cov.: 33 AF XY: 0.191 AC XY: 14191 AN XY: 74410

African (AFR) AF: 0.0681 AC: 2830 AN: 41554

American (AMR) AF: 0.238 AC: 3631 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1410 AN: 5176

South Asian (SAS) AF: 0.369 AC: 1777 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2741 AN: 10576

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14374 AN: 68004

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.199 Hom.: 10707

Bravo AF: 0.170

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.57
DANN	Benign	0.60
PhyloP100		-0.088

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: rs2013486; hg19: chr11-12149531;