Genetic Variant ENST00000561815.5:c.100A>C (chr16-30183126-A-C) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The ENST00000561815.5(CORO1A):c.100A>C(p.Arg34Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 424,950 control chromosomes in the GnomAD database, including 1,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 215 hom., cov: 32)

Exomes 𝑓: 0.024 ( 839 hom. )

Consequence

CORO1A
ENST00000561815.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.114

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 16-30183126-A-C is Benign according to our data. Variant chr16-30183126-A-C is described in ClinVar as [Benign]. Clinvar id is 2688464.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.114 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO1A	ENST00000561815.5 link	c.100A>C	p.Arg34Arg	synonymous_variant	Exon 1 of 5	5		ENSP00000456756.1		H3BSL1
CORO1A	ENST00000563778.5 link	c.-2+113A>C		intron_variant	Intron 1 of 5	5		ENSP00000456266.1		H3BRJ0

Frequencies

GnomAD3 genomes

AF:

0.0169

AC:

2562

AN:

152034

Hom.:

214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00251

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0576

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.00804

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000809

Gnomad OTH

AF:

0.0148

GnomAD3 exomes

AF:

0.0561

AC:

5628

AN:

100370

Hom.:

717

AF XY:

0.0424

AC XY:

2387

AN XY:

56354

show subpopulations

Gnomad AFR exome

AF:

0.00232

Gnomad AMR exome

AF:

0.240

Gnomad ASJ exome

AF:

0.000572

Gnomad EAS exome

AF:

0.0566

Gnomad SAS exome

AF:

0.00323

Gnomad FIN exome

AF:

0.00745

Gnomad NFE exome

AF:

0.000603

Gnomad OTH exome

AF:

0.0297

GnomAD4 exome

AF:

0.0242

AC:

6615

AN:

272798

Hom.:

839

Cov.:

AF XY:

0.0185

AC XY:

2905

AN XY:

157432

show subpopulations

Gnomad4 AFR exome

AF:

0.00226

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.000516

Gnomad4 EAS exome

AF:

0.0528

Gnomad4 SAS exome

AF:

0.00302

Gnomad4 FIN exome

AF:

0.00682

Gnomad4 NFE exome

AF:

0.000753

Gnomad4 OTH exome

AF:

0.0106

GnomAD4 genome

AF:

0.0169

AC:

2567

AN:

152152

Hom.:

215

Cov.:

AF XY:

0.0191

AC XY:

1419

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.00250

Gnomad4 AMR

AF:

0.129

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0575

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00804

Gnomad4 NFE

AF:

0.000809

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.00236

Hom.:

Bravo

AF:

0.0277

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

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 28% of patients studied by a panel of primary immunodeficiencies. Number of patients: 25. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.6

DANN

Benign

0.41

Splicing

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