Genetic Variant NM_004371.4:c.3615+49A>G (chr1-160290443-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004371.4(COPA):c.3615+49A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,567,586 control chromosomes in the GnomAD database, including 194,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14904 hom., cov: 31)

Exomes 𝑓: 0.50 ( 179412 hom. )

Consequence

COPA
NM_004371.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.122

Variant links:

Genes affected

COPA (HGNC:2230): (COPI coat complex subunit alpha) In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COPs). Seven coat proteins have been identified, and they represent subunits of a complex known as coatomer. The subunits are designated alpha-COP, beta-COP, beta-prime-COP, gamma-COP, delta-COP, epsilon-COP, and zeta-COP. The alpha-COP, encoded by COPA, shares high sequence similarity with RET1P, the alpha subunit of the coatomer complex in yeast. Also, the N-terminal 25 amino acids of alpha-COP encode the bioactive peptide, xenin, which stimulates exocrine pancreatic secretion and may act as a gastrointestinal hormone. Alternative splicing results in multiple splice forms encoding distinct isoforms. [provided by RefSeq, Jul 2008]

COPA links:

LOC107985219 (HGNC:):

LOC107985219 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 1-160290443-T-C is Benign according to our data. Variant chr1-160290443-T-C is described in ClinVar as [Benign]. Clinvar id is 2628122.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
COPA	NM_004371.4 link	c.3615+49A>G	intron_variant	Intron 32 of 32	ENST00000241704.8	NP_004362.2	P53621-1
COPA	NM_001098398.2 link	c.3642+49A>G	intron_variant	Intron 32 of 32		NP_001091868.1	P53621-2
LOC107985219	XR_001738265.2 link	n.537-814T>C	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPA	ENST00000241704.8 link	c.3615+49A>G		intron_variant	Intron 32 of 32	1	NM_004371.4	ENSP00000241704.7		P53621-1

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65043

AN:

151796

Hom.:

14905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.533

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.498

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.460

GnomAD3 exomes

AF:

0.480

AC:

109495

AN:

227936

Hom.:

27240

AF XY:

0.492

AC XY:

60683

AN XY:

123370

show subpopulations

Gnomad AFR exome

AF:

0.248

Gnomad AMR exome

AF:

0.481

Gnomad ASJ exome

AF:

0.440

Gnomad EAS exome

AF:

0.355

Gnomad SAS exome

AF:

0.617

Gnomad FIN exome

AF:

0.488

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.490

GnomAD4 exome

AF:

0.500

AC:

707195

AN:

1415670

Hom.:

179412

Cov.:

AF XY:

0.503

AC XY:

352835

AN XY:

701400

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.483

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.365

Gnomad4 SAS exome

AF:

0.610

Gnomad4 FIN exome

AF:

0.476

Gnomad4 NFE exome

AF:

0.507

Gnomad4 OTH exome

AF:

0.484

GnomAD4 genome

AF:

0.428

AC:

65067

AN:

151916

Hom.:

14904

Cov.:

AF XY:

0.430

AC XY:

31937

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.469

Gnomad4 ASJ

AF:

0.422

Gnomad4 EAS

AF:

0.342

Gnomad4 SAS

AF:

0.609

Gnomad4 FIN

AF:

0.498

Gnomad4 NFE

AF:

0.504

Gnomad4 OTH

AF:

0.462

Alfa

AF:

0.454

Hom.:

2974

Bravo

AF:

0.419

Asia WGS

AF:

0.473

AC:

1646

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

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 74% of patients studied by a panel of primary immunodeficiencies. Number of patients: 71. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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