NM_052820.4:c.1-16171A>G

Variant names:

• chr9-98173831-T-C
• rs1985859
• NM_052820.4:c.1-16171A>G

Variant summary

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

The NM_052820.4(CORO2A):​c.1-16171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,782 control chromosomes in the GnomAD database, including 5,900 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 0.27 (5900 hom., cov: 32)
• Consequence: CORO2A NM_052820.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 7 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052820.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO2A	NM_052820.4	MANE Select	c.1-16171A>G		intron	N/A	NP_438171.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO2A	ENST00000375077.5	TSL:1 MANE Select	c.1-16171A>G		intron	N/A	ENSP00000364218.4

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41550 AN: 151662 Hom.: 5893 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.274 AC: 41574 AN: 151782 Hom.: 5900 Cov.: 32 AF XY: 0.277 AC XY: 20555 AN XY: 74190

African (AFR) AF: 0.299 AC: 12358 AN: 41384

American (AMR) AF: 0.241 AC: 3686 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1180 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2522 AN: 5158

South Asian (SAS) AF: 0.280 AC: 1347 AN: 4810

European-Finnish (FIN) AF: 0.298 AC: 3145 AN: 10536

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16393 AN: 67860

Other (OTH) AF: 0.286 AC: 601 AN: 2104

Alfa AF: 0.250 Hom.: 2006

Bravo AF: 0.272

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1985859; hg19: chr9-100936113;