9-98148411-T-A

Position:

• chr9-98148411-T-A

Variant summary

Our verdict is Benign. Variant got -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

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=-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 male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 53 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CORO2A	NM_052820.4	c.201+9049A>T		intron_variant		ENST00000375077.5	NP_438171.1
CORO2A	NM_003389.3	c.201+9049A>T		intron_variant			NP_003380.3
CORO2A	XM_011518986.4	c.201+9049A>T		intron_variant			XP_011517288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORO2A	ENST00000375077.5	c.201+9049A>T		intron_variant		1	NM_052820.4	ENSP00000364218.4
CORO2A	ENST00000343933.9	c.201+9049A>T		intron_variant		1		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

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.00887

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.000267

Gnomad4 SAS AF: 0.00553

Gnomad4 FIN AF: 0.00351

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.17

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

Publications

LitVar

Other links and lift over

dbSNP: rs7865848; hg19: chr9-100910693;