rs9806222

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.101
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
CORO2BNM_006091.5 linkuse as main transcriptc.15+12588G>A intron_variant ENST00000261861.10 NP_006082.3 Q9UQ03-1
CORO2BNM_001324014.1 linkuse as main transcriptc.1-53295G>A intron_variant NP_001310943.1 Q9UQ03-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CORO2BENST00000261861.10 linkuse as main transcriptc.15+12588G>A intron_variant 1 NM_006091.5 ENSP00000261861.6 Q9UQ03-1

Frequencies

GnomAD3 genomes
AF:
0.515
AC:
78264
AN:
151900
Hom.:
20511
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.473
Gnomad4 AMR
AF:
0.579
Gnomad4 ASJ
AF:
0.506
Gnomad4 EAS
AF:
0.769
Gnomad4 SAS
AF:
0.677
Gnomad4 FIN
AF:
0.533
Gnomad4 NFE
AF:
0.496
Gnomad4 OTH
AF:
0.514
Alfa
AF:
0.505
Hom.:
19704
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9806222; hg19: chr15-68884204; API