Variant 15-68711639-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_006091.5(CORO2B):c.581T>A(p.Leu194Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,614,128 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 7 hom. )

Consequence

CORO2B
NM_006091.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.92

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]

CORO2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.07330099).

BP6

Variant 15-68711639-T-A is Benign according to our data. Variant chr15-68711639-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2645492.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd at 388 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO2B	NM_006091.5 linkuse as main transcript	c.581T>A	p.Leu194Gln	missense_variant	5/12	ENST00000261861.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CORO2B	ENST00000261861.10 linkuse as main transcript	c.581T>A	p.Leu194Gln	missense_variant	5/12	1	NM_006091.5	P4	Q9UQ03-1
CORO2B	ENST00000540068.6 linkuse as main transcript	c.566T>A	p.Leu189Gln	missense_variant	5/12	5		A1	Q9UQ03-2
CORO2B	ENST00000543950.3 linkuse as main transcript	c.566T>A	p.Leu189Gln	missense_variant	5/12	2		A1	Q9UQ03-2

Frequencies

GnomAD3 genomes

AF:

0.00255

AC:

388

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000458

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00549

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00348

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00338

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00251

AC:

631

AN:

251194

Hom.:

AF XY:

0.00261

AC XY:

355

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00345

Gnomad ASJ exome

AF:

0.00407

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00365

Gnomad NFE exome

AF:

0.00311

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00257

AC:

3751

AN:

1461798

Hom.:

Cov.:

AF XY:

0.00252

AC XY:

1829

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.000418

Gnomad4 AMR exome

AF:

0.00400

Gnomad4 ASJ exome

AF:

0.00402

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000197

Gnomad4 FIN exome

AF:

0.00313

Gnomad4 NFE exome

AF:

0.00281

Gnomad4 OTH exome

AF:

0.00229

GnomAD4 genome

AF:

0.00255

AC:

388

AN:

152330

Hom.:

Cov.:

AF XY:

0.00255

AC XY:

190

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.000457

Gnomad4 AMR

AF:

0.00549

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00348

Gnomad4 NFE

AF:

0.00338

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00339

Hom.:

Bravo

AF:

0.00254

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.000909

AC:

ESP6500EA

AF:

0.00361

AC:

ExAC

AF:

0.00266

AC:

323

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00333

EpiControl

AF:

0.00403

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

CORO2B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.024

BayesDel_noAF

Pathogenic

0.20

Cadd

Pathogenic

Dann

Uncertain

0.99

DEOGEN2

Benign

0.18

T;.;.;.

Eigen

Pathogenic

0.69

Eigen_PC

Pathogenic

0.68

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.95

D;.;.;D

M_CAP

Benign

0.064

MetaRNN

Benign

0.073

T;T;T;T

MetaSVM

Benign

-0.37

MutationAssessor

Uncertain

2.4

M;.;.;.

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Uncertain

0.73

PROVEAN

Pathogenic

-4.5

D;D;D;D

Sift

Benign

0.095

T;T;T;T

Sift4G

Benign

0.38

T;T;T;T

Polyphen

0.99

D;.;.;.

Vest4

0.93

MVP

0.87

MPC

1.5

ClinPred

0.019

GERP RS

5.7

Varity_R

0.62

gMVP

0.76

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over