17-80181089-TAAAA-TAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001366385.1(CARD14):​c.-20-318_-20-316dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0043 ( 4 hom., cov: 20)

Consequence

CARD14
NM_001366385.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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 -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00428 (605/141470) while in subpopulation EAS AF= 0.0233 (113/4860). AF 95% confidence interval is 0.0198. There are 4 homozygotes in gnomad4. There are 315 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
BS2
High AC in GnomAd4 at 605 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CARD14NM_001366385.1 linkc.-20-318_-20-316dupAAA 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.-20-330_-20-329insAAA intron_variant Intron 4 of 23 NM_001366385.1 ENSP00000498071.1 Q9BXL6-1

Frequencies

GnomAD3 genomes
AF:
0.00423
AC:
598
AN:
141422
Hom.:
4
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.00871
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00220
Gnomad ASJ
AF:
0.00781
Gnomad EAS
AF:
0.0230
Gnomad SAS
AF:
0.00157
Gnomad FIN
AF:
0.00191
Gnomad MID
AF:
0.00662
Gnomad NFE
AF:
0.000884
Gnomad OTH
AF:
0.00514
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00428
AC:
605
AN:
141470
Hom.:
4
Cov.:
20
AF XY:
0.00461
AC XY:
315
AN XY:
68330
show subpopulations
Gnomad4 AFR
AF:
0.00885
Gnomad4 AMR
AF:
0.00220
Gnomad4 ASJ
AF:
0.00781
Gnomad4 EAS
AF:
0.0233
Gnomad4 SAS
AF:
0.00158
Gnomad4 FIN
AF:
0.00191
Gnomad4 NFE
AF:
0.000884
Gnomad4 OTH
AF:
0.00511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs60307812; hg19: chr17-78154888; API