dbSNP rs17477949: MICAL2:c.265-6594C>T (chr11-12197656-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001282663.2(MICAL2):c.265-6594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,160 control chromosomes in the GnomAD database, including 8,134 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 0.29 ( 8134 hom., cov: 33)

Exomes 𝑓: 0.31 ( 0 hom. )

Consequence

MICAL2
NM_001282663.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.362

Publications

2 publications found

Variant links:

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]

MICAL2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MICAL2	NM_001282663.2	MANE Select	c.265-6594C>T	intron	N/A	NP_001269592.1	O94851-1
MICAL2	NM_001393937.1		c.265-6594C>T	intron	N/A	NP_001380866.1	O94851-7
MICAL2	NM_001346292.2		c.265-6594C>T	intron	N/A	NP_001333221.1	O94851-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MICAL2	ENST00000683283.1	MANE Select	c.265-6594C>T	intron	N/A	ENSP00000507067.1	O94851-1
MICAL2	ENST00000256194.8	TSL:1	c.265-6594C>T	intron	N/A	ENSP00000256194.4	O94851-1
MICAL2	ENST00000528931.5	TSL:1	c.265-6594C>T	intron	N/A	ENSP00000499778.1	O94851-6

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44861

AN:

152014

Hom.:

8138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0922

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.0577

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.328

GnomAD4 exome

AF:

0.308

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.295

AC:

44858

AN:

152134

Hom.:

8134

Cov.:

AF XY:

0.292

AC XY:

21700

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.0920

AC:

3819

AN:

41524

American (AMR)

AF:

0.329

AC:

5033

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.434

AC:

1507

AN:

3470

East Asian (EAS)

AF:

0.0580

AC:

300

AN:

5168

South Asian (SAS)

AF:

0.363

AC:

1751

AN:

4822

European-Finnish (FIN)

AF:

0.324

AC:

3432

AN:

10578

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.409

AC:

27817

AN:

67972

Other (OTH)

AF:

0.323

AC:

683

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1507

3014

4520

6027

7534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.372

Hom.:

14556

Bravo

AF:

0.283

Asia WGS

AF:

0.201

AC:

701

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.1

(source)

DANN

Benign

0.39

PhyloP100

-0.36

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over