16-30183126-A-C

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

2

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]

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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
CORO1AENST00000561815.5 linkc.100A>C p.Arg34Arg synonymous_variant Exon 1 of 5 5 ENSP00000456756.1 H3BSL1
CORO1AENST00000563778.5 linkc.-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.:
32
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.:
0
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.:
32
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.:
5
Bravo
AF:
0.0277
Asia WGS
AF:
0.0220
AC:
77
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJan 24, 2024This 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.

Other links and lift over

dbSNP: rs74183730; hg19: chr16-30194447; API