NM_001366385.1:c.-20-318_-20-316dupAAA

Variant names:

• chr17-80181089-T-TAAA
• rs60307812
• NM_001366385.1:c.-20-318_-20-316dupAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511

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]

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 20. This position passed quality control check.
• BS2: High AC in GnomAd4 at 605 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARD14	NM_001366385.1	c.-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
CARD14	ENST00000648509.2	c.-20-330_-20-329insAAA		intron_variant	Intron 4 of 23		NM_001366385.1	ENSP00000498071.1

Frequencies

GnomAD3 genomes AF: 0.00423 AC: 598 AN: 141422 Hom.: 4 Cov.: 20

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

African (AFR) AF: 0.00885 AC: 343 AN: 38772

American (AMR) AF: 0.00220 AC: 31 AN: 14086

Ashkenazi Jewish (ASJ) AF: 0.00781 AC: 26 AN: 3330

East Asian (EAS) AF: 0.0233 AC: 113 AN: 4860

South Asian (SAS) AF: 0.00158 AC: 7 AN: 4438

European-Finnish (FIN) AF: 0.00191 AC: 16 AN: 8392

Middle Eastern (MID) AF: 0.00719 AC: 2 AN: 278

European-Non Finnish (NFE) AF: 0.000884 AC: 57 AN: 64490

Other (OTH) AF: 0.00511 AC: 10 AN: 1956

Alfa AF: 0.00 Hom.: 106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs60307812; hg19: chr17-78154888;