9-98176180-C-T

Variant names:

• chr9-98176180-C-T
• rs10985325
• NM_052820.4:c.-1+16379G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052820.4(CORO2A):​c.-1+16379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,130 control chromosomes in the GnomAD database, including 1,752 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 0.14 (1752 hom., cov: 32)
• Consequence: CORO2A NM_052820.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CORO2A	NM_052820.4	c.-1+16379G>A		intron_variant	Intron 1 of 11	ENST00000375077.5	NP_438171.1
CORO2A	XM_011518986.4	c.-1+9253G>A		intron_variant	Intron 1 of 11		XP_011517288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO2A	ENST00000375077.5	c.-1+16379G>A		intron_variant	Intron 1 of 11	1	NM_052820.4	ENSP00000364218.4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21219 AN: 152010 Hom.: 1749 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.140 AC: 21246 AN: 152130 Hom.: 1752 Cov.: 32 AF XY: 0.145 AC XY: 10755 AN XY: 74380

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.133

Alfa AF: 0.141 Hom.: 1019

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.041
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10985325; hg19: chr9-100938462;