16-30186830-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_007074.4(CORO1A):c.336A>G(p.Pro112Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 1,610,452 control chromosomes in the GnomAD database, including 281,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 36953 hom., cov: 33)

Exomes 𝑓: 0.57 ( 244134 hom. )

Consequence

CORO1A
NM_007074.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7O:1

Conservation

PhyloP100: -6.22

Publications

39 publications found

Variant links:

Genes affected

CORO1A (HGNC:2252): (coronin 1A) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Alternative splicing results in multiple transcript variants. A related pseudogene has been defined on chromosome 16. [provided by RefSeq, Sep 2010]

CORO1A Gene-Disease associations (from GenCC):

severe combined immunodeficiency due to CORO1A deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Ambry Genetics
epidermodysplasia verruciformis
Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
autism spectrum disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

CORO1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 16-30186830-A-G is Benign according to our data. Variant chr16-30186830-A-G is described in ClinVar as Benign. ClinVar VariationId is 379386.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-6.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CORO1A	NM_007074.4 link	c.336A>G	p.Pro112Pro	synonymous_variant	Exon 4 of 11	ENST00000219150.10	NP_009005.1	P31146A0A024R611
CORO1A	NM_001193333.3 link	c.336A>G	p.Pro112Pro	synonymous_variant	Exon 5 of 12		NP_001180262.1	P31146A0A024R611

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO1A	ENST00000219150.10 link	c.336A>G	p.Pro112Pro	synonymous_variant	Exon 4 of 11	1	NM_007074.4	ENSP00000219150.6		P31146

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102901

AN:

151998

Hom.:

36885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.693

Gnomad ASJ

AF:

0.671

Gnomad EAS

AF:

0.930

Gnomad SAS

AF:

0.706

Gnomad FIN

AF:

0.617

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.656

GnomAD2 exomes

AF:

0.654

AC:

161348

AN:

246798

AF XY:

0.642

show subpopulations

Gnomad AFR exome

AF:

0.906

Gnomad AMR exome

AF:

0.772

Gnomad ASJ exome

AF:

0.660

Gnomad EAS exome

AF:

0.931

Gnomad FIN exome

AF:

0.602

Gnomad NFE exome

AF:

0.540

Gnomad OTH exome

AF:

0.624

GnomAD4 exome

AF:

0.569

AC:

830073

AN:

1458336

Hom.:

244134

Cov.:

AF XY:

0.571

AC XY:

414203

AN XY:

725694

show subpopulations

African (AFR)

AF:

0.909

AC:

30429

AN:

33476

American (AMR)

AF:

0.760

AC:

33968

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.657

AC:

17174

AN:

26132

East Asian (EAS)

AF:

0.903

AC:

35854

AN:

39696

South Asian (SAS)

AF:

0.680

AC:

58661

AN:

86244

European-Finnish (FIN)

AF:

0.609

AC:

30496

AN:

50086

Middle Eastern (MID)

AF:

0.633

AC:

3631

AN:

5740

European-Non Finnish (NFE)

AF:

0.525

AC:

583323

AN:

1111890

Other (OTH)

AF:

0.605

AC:

36537

AN:

60364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

22501

45001

67502

90002

112503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16940

33880

50820

67760

84700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.677

AC:

103032

AN:

152116

Hom.:

36953

Cov.:

AF XY:

0.683

AC XY:

50772

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.894

AC:

37123

AN:

41522

American (AMR)

AF:

0.693

AC:

10595

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.671

AC:

2327

AN:

3470

East Asian (EAS)

AF:

0.930

AC:

4791

AN:

5154

South Asian (SAS)

AF:

0.706

AC:

3406

AN:

4826

European-Finnish (FIN)

AF:

0.617

AC:

6528

AN:

10586

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.534

AC:

36278

AN:

67958

Other (OTH)

AF:

0.661

AC:

1395

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1560

3120

4681

6241

7801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.574

Hom.:

37861

Bravo

AF:

0.699

Asia WGS

AF:

0.835

AC:

2901

AN:

3478

EpiCase

AF:

0.556

EpiControl

AF:

0.552

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Oct 20, 2015

GeneDx

Significance:Benign

Review Status:flagged submission

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 83% of patients studied by a panel of primary immunodeficiencies. Number of patients: 80. Only high quality variants are reported. -

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:2Other:1

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Jan 05, 2022

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Severe combined immunodeficiency due to CORO1A deficiency

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.095

(source)

DANN

Benign

0.58

PhyloP100

-6.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over