Genetic Variant CORO2A:c.201+9049A>T (chr9-98148411-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_052820.4(CORO2A):c.201+9049A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 111,004 control chromosomes in the GnomAD database, including 53 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 0.021 ( 53 hom., cov: 29)

Consequence

CORO2A
NM_052820.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02

Publications

1 publications found

Variant links:

Genes affected

CORO2A (HGNC:2255): (coronin 2A) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein contains 5 WD repeats, and has a structural similarity with actin-binding proteins: the D. discoideum coronin and the human p57 protein, suggesting that this protein may also be an actin-binding protein that regulates cell motility. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]

CORO2A 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=-1.0).

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0207 (2301/111004) while in subpopulation AFR AF = 0.0502 (1492/29706). AF 95% confidence interval is 0.0481. There are 53 homozygotes in GnomAd4. There are 1083 alleles in the male GnomAd4 subpopulation. Median coverage is 29. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 53 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
CORO2A	NM_052820.4 link	c.201+9049A>T	intron_variant	Intron 2 of 11	ENST00000375077.5	NP_438171.1
CORO2A	NM_003389.3 link	c.201+9049A>T	intron_variant	Intron 2 of 11		NP_003380.3
CORO2A	XM_011518986.4 link	c.201+9049A>T	intron_variant	Intron 2 of 11		XP_011517288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO2A	ENST00000375077.5 link	c.201+9049A>T		intron_variant	Intron 2 of 11	1	NM_052820.4	ENSP00000364218.4
CORO2A	ENST00000343933.9 link	c.201+9049A>T		intron_variant	Intron 2 of 11	1		ENSP00000343746.5

Frequencies

GnomAD3 genomes

AF:

0.0207

AC:

2295

AN:

110964

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0501

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00897

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.000266

Gnomad SAS

AF:

0.00551

Gnomad FIN

AF:

0.00351

Gnomad MID

AF:

0.00980

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.0156

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

GnomAD4 genome

AF:

0.0207

AC:

2301

AN:

111004

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

1083

AN XY:

53714

show subpopulations

African (AFR)

AF:

0.0502

AC:

1492

AN:

29706

American (AMR)

AF:

0.00887

AC:

AN:

10826

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

2750

East Asian (EAS)

AF:

0.000267

AC:

AN:

3742

South Asian (SAS)

AF:

0.00553

AC:

AN:

3436

European-Finnish (FIN)

AF:

0.00351

AC:

AN:

6262

Middle Eastern (MID)

AF:

0.0106

AC:

AN:

188

European-Non Finnish (NFE)

AF:

0.0116

AC:

600

AN:

51872

Other (OTH)

AF:

0.0155

AC:

AN:

1552

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

177

265

354

442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.55

(source)

DANN

Benign

0.17

PhyloP100

-3.0

Mutation Taster

=100/0

polymorphism

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over