9-98189556-G-T

Variant names:

• chr9-98189556-G-T
• rs7870439
• NM_052820.4:c.-1+3003C>A

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+3003C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,108 control chromosomes in the GnomAD database, including 4,304 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 0.24 (4304 hom., cov: 33)
• Consequence: CORO2A NM_052820.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 9 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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+3003C>A		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+3003C>A		intron	N/A	ENSP00000364218.4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35805 AN: 151992 Hom.: 4307 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.235 AC: 35805 AN: 152108 Hom.: 4304 Cov.: 33 AF XY: 0.230 AC XY: 17122 AN XY: 74346

African (AFR) AF: 0.249 AC: 10343 AN: 41492

American (AMR) AF: 0.214 AC: 3266 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.148 AC: 767 AN: 5176

South Asian (SAS) AF: 0.203 AC: 977 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2051 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16421 AN: 67976

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.237 Hom.: 16308

Bravo AF: 0.236

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.78
PhyloP100		1.8
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: rs7870439; hg19: chr9-100951838;