15-68577243-C-G

Position:

• chr15-68577243-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001324014.1(CORO2B):​c.-1+41584C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,216 control chromosomes in the GnomAD database, including 64,522 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 0.92 (64522 hom., cov: 31)
• Consequence: CORO2B NM_001324014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CORO2B	NM_001324014.1	c.-1+41584C>G		intron_variant			NP_001310943.1
		n.68577243C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139738 AN: 152098 Hom.: 64472 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.919 AC: 139848 AN: 152216 Hom.: 64522 Cov.: 31 AF XY: 0.922 AC XY: 68620 AN XY: 74418

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.929

Alfa AF: 0.933 Hom.: 2226

Bravo AF: 0.913

Asia WGS AF: 0.973 AC: 3383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs615188; hg19: chr15-68869582;