ENST00000571861.5:n.149G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000571861.5(CARD14):n.149G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,604,012 control chromosomes in the GnomAD database, including 94,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7599 hom., cov: 32)

Exomes 𝑓: 0.34 ( 86444 hom. )

Consequence

CARD14
ENST00000571861.5 non_coding_transcript_exon

Scores

Splicing: ADA: 0.0001668

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6O:1

Conservation

PhyloP100: 0.0180

Publications

16 publications found

Variant links:

Genes affected

CARD14 (HGNC:16446): (caspase recruitment domain family member 14) This gene encodes a caspase recruitment domain-containing protein that is a member of the membrane-associated guanylate kinase (MAGUK) family of proteins. Members of this protein family are scaffold proteins that are involved in a diverse array of cellular processes including cellular adhesion, signal transduction and cell polarity control. This protein has been shown to specifically interact with BCL10, a protein known to function as a positive regulator of cell apoptosis and NF-kappaB activation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]

CARD14 Gene-Disease associations (from GenCC):

familial pityriasis rubra pilaris
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp
psoriasis 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

CARD14 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-80188371-G-A is Benign according to our data. Variant chr17-80188371-G-A is described in ClinVar as Benign. ClinVar VariationId is 402484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARD14	NM_001366385.1 link	c.676-6G>A		splice_region_variant, intron_variant	Intron 7 of 23	ENST00000648509.2	NP_001353314.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARD14	ENST00000648509.2 link	c.676-6G>A		splice_region_variant, intron_variant	Intron 7 of 23		NM_001366385.1	ENSP00000498071.1		Q9BXL6-1

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46494

AN:

151920

Hom.:

7596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.315

GnomAD2 exomes

AF:

0.329

AC:

79366

AN:

240926

AF XY:

0.335

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.260

Gnomad ASJ exome

AF:

0.409

Gnomad EAS exome

AF:

0.400

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.348

Gnomad OTH exome

AF:

0.340

GnomAD4 exome

AF:

0.343

AC:

497387

AN:

1451972

Hom.:

86444

Cov.:

AF XY:

0.342

AC XY:

247135

AN XY:

722104

show subpopulations

African (AFR)

AF:

0.200

AC:

6606

AN:

33050

American (AMR)

AF:

0.263

AC:

11434

AN:

43428

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

10773

AN:

25962

East Asian (EAS)

AF:

0.427

AC:

16508

AN:

38682

South Asian (SAS)

AF:

0.287

AC:

24324

AN:

84656

European-Finnish (FIN)

AF:

0.386

AC:

20500

AN:

53114

Middle Eastern (MID)

AF:

0.376

AC:

2159

AN:

5744

European-Non Finnish (NFE)

AF:

0.347

AC:

384665

AN:

1107326

Other (OTH)

AF:

0.340

AC:

20418

AN:

60010

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

15266

30531

45797

61062

76328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12298

24596

36894

49192

61490

<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:

0.306

AC:

46507

AN:

152040

Hom.:

7599

Cov.:

AF XY:

0.307

AC XY:

22787

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.202

AC:

8360

AN:

41454

American (AMR)

AF:

0.275

AC:

4199

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1412

AN:

3466

East Asian (EAS)

AF:

0.399

AC:

2062

AN:

5168

South Asian (SAS)

AF:

0.297

AC:

1432

AN:

4824

European-Finnish (FIN)

AF:

0.405

AC:

4280

AN:

10572

Middle Eastern (MID)

AF:

0.395

AC:

116

AN:

294

European-Non Finnish (NFE)

AF:

0.347

AC:

23606

AN:

67960

Other (OTH)

AF:

0.316

AC:

668

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1631

3261

4892

6522

8153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.329

Hom.:

9094

Bravo

AF:

0.295

Asia WGS

AF:

0.324

AC:

1125

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

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 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 46. Only high quality variants are reported. -

Mar 29, 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:1Other:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

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. -

Pityriasis rubra pilaris

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Psoriasis 2

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Pityriasis rubra pilaris;C1864497:Psoriasis 2

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.85

CADD

Benign

4.5

(source)

DANN

Benign

0.52

PhyloP100

0.018

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00017

dbscSNV1_RF

Benign

0.036

SpliceAI score (max)

0.13

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