chr17-80181089-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001366385.1(CARD14):​c.-20-316delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.034 ( 205 hom., cov: 20)

Consequence

CARD14
NM_001366385.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.511
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 17-80181089-TA-T is Benign according to our data. Variant chr17-80181089-TA-T is described in ClinVar as [Benign]. Clinvar id is 1283751.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CARD14NM_001366385.1 linkc.-20-316delA intron_variant Intron 4 of 23 ENST00000648509.2 NP_001353314.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CARD14ENST00000648509.2 linkc.-20-329delA intron_variant Intron 4 of 23 NM_001366385.1 ENSP00000498071.1 Q9BXL6-1

Frequencies

GnomAD3 genomes
AF:
0.0342
AC:
4832
AN:
141168
Hom.:
205
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.108
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0208
Gnomad ASJ
AF:
0.0174
Gnomad EAS
AF:
0.00184
Gnomad SAS
AF:
0.00314
Gnomad FIN
AF:
0.00624
Gnomad MID
AF:
0.0166
Gnomad NFE
AF:
0.00286
Gnomad OTH
AF:
0.0264
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0342
AC:
4836
AN:
141216
Hom.:
205
Cov.:
20
AF XY:
0.0339
AC XY:
2309
AN XY:
68202
show subpopulations
Gnomad4 AFR
AF:
0.108
Gnomad4 AMR
AF:
0.0208
Gnomad4 ASJ
AF:
0.0174
Gnomad4 EAS
AF:
0.00185
Gnomad4 SAS
AF:
0.00293
Gnomad4 FIN
AF:
0.00624
Gnomad4 NFE
AF:
0.00286
Gnomad4 OTH
AF:
0.0262

ClinVar

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

Submissions by phenotype

not provided Benign:1
Oct 06, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs60307812; hg19: chr17-78154888; API