rs10831759

Variant names:

• chr11-12199835-A-G
• rs10831759
• NM_001282663.2:c.265-4415A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001393937.1(MICAL2):​c.265-4415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,128 control chromosomes in the GnomAD database, including 1,004 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 0.11 (1004 hom., cov: 32)
• Consequence: MICAL2 NM_001393937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393937.1. 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.265-4415A>G		intron	N/A	NP_001269592.1
	MICAL2	NM_001393937.1		c.265-4415A>G		intron	N/A	NP_001380866.1
	MICAL2	NM_001346292.2		c.265-4415A>G		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.265-4415A>G		intron	N/A	ENSP00000507067.1
	MICAL2	ENST00000256194.8	TSL:1	c.265-4415A>G		intron	N/A	ENSP00000256194.4
	MICAL2	ENST00000528931.5	TSL:1	c.265-4415A>G		intron	N/A	ENSP00000499778.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16549 AN: 152010 Hom.: 1005 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0851

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.109 AC: 16565 AN: 152128 Hom.: 1004 Cov.: 32 AF XY: 0.109 AC XY: 8110 AN XY: 74392

African (AFR) AF: 0.157 AC: 6530 AN: 41476

American (AMR) AF: 0.157 AC: 2400 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0851 AC: 295 AN: 3468

East Asian (EAS) AF: 0.102 AC: 526 AN: 5170

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4814

European-Finnish (FIN) AF: 0.0626 AC: 663 AN: 10598

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.0835 AC: 5679 AN: 68004

Other (OTH) AF: 0.117 AC: 247 AN: 2110

Alfa AF: 0.0882 Hom.: 821

Bravo AF: 0.118

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		-0.37

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: rs10831759; hg19: chr11-12221382;