rs1994318

Variant names:

• chr11-12138114-C-A
• rs1994318
• NM_001282663.2:c.-148-276C>A

Variant summary

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

The NM_001282663.2(MICAL2):​c.-148-276C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,066 control chromosomes in the GnomAD database, including 21,915 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 0.52 (21915 hom., cov: 34)
• Consequence: MICAL2 NM_001282663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 10 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICAL2	NM_001282663.2	c.-148-276C>A		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.-148-276C>A		intron_variant	Intron 1 of 27		NM_001282663.2	ENSP00000507067.1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79272 AN: 151948 Hom.: 21913 Cov.: 34

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.521 AC: 79288 AN: 152066 Hom.: 21915 Cov.: 34 AF XY: 0.516 AC XY: 38342 AN XY: 74340

African (AFR) AF: 0.331 AC: 13755 AN: 41502

American (AMR) AF: 0.487 AC: 7432 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2272 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2568 AN: 5168

South Asian (SAS) AF: 0.390 AC: 1884 AN: 4828

European-Finnish (FIN) AF: 0.571 AC: 6015 AN: 10530

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43327 AN: 67976

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.595 Hom.: 65920

Bravo AF: 0.511

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.49
DANN	Benign	0.81
PhyloP100		-0.58
PromoterAI		0.0085	Neutral

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: rs1994318; hg19: chr11-12159661;