rs7870439

Positions:

• chr9-98189556-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CORO2A	NM_052820.4	c.-1+3003C>A		intron_variant		ENST00000375077.5	NP_438171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORO2A	ENST00000375077.5	c.-1+3003C>A		intron_variant		1	NM_052820.4	ENSP00000364218	P1

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

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.250

Alfa AF: 0.238 Hom.: 6921

Bravo AF: 0.236

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7870439; hg19: chr9-100951838;