11-12275234-T-G

Variant names:

• chr11-12275234-T-G
• rs7106205
• NM_001393937.1:c.3335-752T>G

Variant summary

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

The NM_001393937.1(MICAL2):​c.3335-752T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,966 control chromosomes in the GnomAD database, including 17,218 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 0.46 (17218 hom., cov: 32)
• Consequence: MICAL2 NM_001393937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICAL2	NM_001393937.1	c.3335-752T>G		intron_variant	Intron 26 of 36		NP_001380866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICAL2	ENST00000646065.2	c.3335-752T>G		intron_variant	Intron 24 of 34			ENSP00000494982.1
MICAL2	ENST00000644505.1	n.382+539T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70427 AN: 151848 Hom.: 17204 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.464 AC: 70466 AN: 151966 Hom.: 17218 Cov.: 32 AF XY: 0.471 AC XY: 35022 AN XY: 74286

African (AFR) AF: 0.491 AC: 20363 AN: 41454

American (AMR) AF: 0.595 AC: 9088 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4260 AN: 5166

South Asian (SAS) AF: 0.546 AC: 2631 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4357 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26943 AN: 67938

Other (OTH) AF: 0.472 AC: 994 AN: 2106

Alfa AF: 0.426 Hom.: 26431

Bravo AF: 0.479

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7106205; hg19: chr11-12296781;