rs10831759

Positions:

• chr11-12199835-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001282663.2(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_001282663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICAL2	NM_001282663.2	c.265-4415A>G		intron_variant		ENST00000683283.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICAL2	ENST00000683283.1	c.265-4415A>G		intron_variant			NM_001282663.2

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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0851

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0357

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0879 Hom.: 712

Bravo AF: 0.118

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10831759; hg19: chr11-12221382;