15-68591865-G-A

Variant names:

• chr15-68591865-G-A
• rs9806222
• NM_006091.5:c.15+12588G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006091.5(CORO2B):​c.15+12588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,018 control chromosomes in the GnomAD database, including 20,548 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 0.52 (20548 hom., cov: 32)
• Consequence: CORO2B NM_006091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 2 publications found

Genes affected

CORO2B (HGNC:2256): (coronin 2B) Enables talin binding activity and vinculin binding activity. Acts upstream of or within several processes, including negative regulation of cell-substrate adhesion; regulation of actin cytoskeleton organization; and regulation of establishment of protein localization. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CORO2B	NM_006091.5	c.15+12588G>A		intron_variant	Intron 1 of 11	ENST00000261861.10	NP_006082.3
CORO2B	NM_001324014.1	c.1-53295G>A		intron_variant	Intron 2 of 12		NP_001310943.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO2B	ENST00000261861.10	c.15+12588G>A		intron_variant	Intron 1 of 11	1	NM_006091.5	ENSP00000261861.6

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78264 AN: 151900 Hom.: 20511 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.515 AC: 78345 AN: 152018 Hom.: 20548 Cov.: 32 AF XY: 0.523 AC XY: 38827 AN XY: 74272

African (AFR) AF: 0.473 AC: 19614 AN: 41478

American (AMR) AF: 0.579 AC: 8845 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3468

East Asian (EAS) AF: 0.769 AC: 3958 AN: 5148

South Asian (SAS) AF: 0.677 AC: 3263 AN: 4820

European-Finnish (FIN) AF: 0.533 AC: 5633 AN: 10570

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33675 AN: 67942

Other (OTH) AF: 0.514 AC: 1085 AN: 2110

Alfa AF: 0.505 Hom.: 25747

Bravo AF: 0.515

Asia WGS AF: 0.716 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.82
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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: rs9806222; hg19: chr15-68884204;