11-12231877-C-T

Variant names:

• chr11-12231877-C-T
• rs1609930
• NM_001282663.2:c.1996-4300C>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.1996-4300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,072 control chromosomes in the GnomAD database, including 5,356 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 0.24 (5356 hom., cov: 33)
• Consequence: MICAL2 NM_001282663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282663.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICAL2	NM_001282663.2	MANE Select	c.1996-4300C>T		intron	N/A	NP_001269592.1
	MICAL2	NM_001393937.1		c.1996-4300C>T		intron	N/A	NP_001380866.1
	MICAL2	NM_001346292.2		c.1996-4300C>T		intron	N/A	NP_001333221.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICAL2	ENST00000683283.1	MANE Select	c.1996-4300C>T		intron	N/A	ENSP00000507067.1
	MICAL2	ENST00000256194.8	TSL:1	c.1996-4300C>T		intron	N/A	ENSP00000256194.4
	MICAL2	ENST00000528931.5	TSL:1	c.1996-4300C>T		intron	N/A	ENSP00000499778.1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36871 AN: 151954 Hom.: 5353 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.243 AC: 36906 AN: 152072 Hom.: 5356 Cov.: 33 AF XY: 0.245 AC XY: 18191 AN XY: 74356

African (AFR) AF: 0.382 AC: 15818 AN: 41436

American (AMR) AF: 0.141 AC: 2162 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2009 AN: 5166

South Asian (SAS) AF: 0.133 AC: 639 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3138 AN: 10572

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12147 AN: 68006

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.180 Hom.: 4758

Bravo AF: 0.239

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.53
PhyloP100		-0.46

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: rs1609930; hg19: chr11-12253424;