17-80181089-TAAAA-TAAAAA

Variant summary

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

The NM_001366385.1(CARD14):​c.-20-316dupA 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 0.030 ( 76 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0303 (4291/141394) while in subpopulation NFE AF= 0.0392 (2528/64444). AF 95% confidence interval is 0.038. There are 76 homozygotes in gnomad4. There are 2055 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
BS2
High AC in GnomAd4 at 4291 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes
AF:
0.0304
AC:
4292
AN:
141346
Hom.:
76
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.00902
Gnomad AMI
AF:
0.0426
Gnomad AMR
AF:
0.0263
Gnomad ASJ
AF:
0.0944
Gnomad EAS
AF:
0.000615
Gnomad SAS
AF:
0.0159
Gnomad FIN
AF:
0.0648
Gnomad MID
AF:
0.0667
Gnomad NFE
AF:
0.0392
Gnomad OTH
AF:
0.0303
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0303
AC:
4291
AN:
141394
Hom.:
76
Cov.:
20
AF XY:
0.0301
AC XY:
2055
AN XY:
68290
show subpopulations
Gnomad4 AFR
AF:
0.00900
Gnomad4 AMR
AF:
0.0263
Gnomad4 ASJ
AF:
0.0944
Gnomad4 EAS
AF:
0.000822
Gnomad4 SAS
AF:
0.0162
Gnomad4 FIN
AF:
0.0648
Gnomad4 NFE
AF:
0.0392
Gnomad4 OTH
AF:
0.0302

ClinVar

Not reported in ClinVar

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