NM_052820.4:c.201+9049A>T

Variant names:

• chr9-98148411-T-A
• rs7865848
• NM_052820.4:c.201+9049A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 1 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=-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

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.201+9049A>T		intron	N/A	NP_438171.1
	CORO2A	NM_003389.3		c.201+9049A>T		intron	N/A	NP_003380.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO2A	ENST00000375077.5	TSL:1 MANE Select	c.201+9049A>T		intron	N/A	ENSP00000364218.4
	CORO2A	ENST00000343933.9	TSL:1	c.201+9049A>T		intron	N/A	ENSP00000343746.5

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 2295 AN: 110964 Hom.: 52 Cov.: 29

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.: 53 Cov.: 29 AF XY: 0.0202 AC XY: 1083 AN XY: 53714

African (AFR) AF: 0.0502 AC: 1492 AN: 29706

American (AMR) AF: 0.00887 AC: 96 AN: 10826

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 45 AN: 2750

East Asian (EAS) AF: 0.000267 AC: 1 AN: 3742

South Asian (SAS) AF: 0.00553 AC: 19 AN: 3436

European-Finnish (FIN) AF: 0.00351 AC: 22 AN: 6262

Middle Eastern (MID) AF: 0.0106 AC: 2 AN: 188

European-Non Finnish (NFE) AF: 0.0116 AC: 600 AN: 51872

Other (OTH) AF: 0.0155 AC: 24 AN: 1552

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.17
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs7865848; hg19: chr9-100910693;