rs11856323

chr15-68600650-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO2B	NM_006091.5	c.15+21373C>T		intron_variant		ENST00000261861.10
CORO2B	NM_001324014.1	c.1-44510C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CORO2B	ENST00000261861.10	c.15+21373C>T		intron_variant		1	NM_006091.5	P4

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

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.0441

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0842 Hom.: 1227

Bravo AF: 0.0777

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.6
Dann	Benign	0.56

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: rs11856323; hg19: chr15-68892989;