rs11856323

Variant names:

• chr15-68600650-C-T
• rs11856323
• NM_006091.5:c.15+21373C>T

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+21373C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,238 control chromosomes in the GnomAD database, including 611 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 0.084 (611 hom., cov: 33)
• Consequence: CORO2B NM_006091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006091.5. 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
	CORO2B	NM_006091.5	MANE Select	c.15+21373C>T		intron	N/A	NP_006082.3
	CORO2B	NM_001324014.1		c.1-44510C>T		intron	N/A	NP_001310943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO2B	ENST00000261861.10	TSL:1 MANE Select	c.15+21373C>T		intron	N/A	ENSP00000261861.6

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12825 AN: 152120 Hom.: 611 Cov.: 33

Gnomad AFR AF: 0.0890

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0843 AC: 12828 AN: 152238 Hom.: 611 Cov.: 33 AF XY: 0.0835 AC XY: 6212 AN XY: 74430

African (AFR) AF: 0.0889 AC: 3690 AN: 41524

American (AMR) AF: 0.0441 AC: 674 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4816

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6292 AN: 68016

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0842 Hom.: 1829

Bravo AF: 0.0777

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.56
PhyloP100		0.027
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: rs11856323; hg19: chr15-68892989;