17-80181089-T-TAAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001366385.1(CARD14):c.-20-319_-20-316dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (2811 hom., cov: 20)
• Consequence: CARD14 NM_001366385.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-80181089-T-TAAAA is Benign according to our data. Variant chr17-80181089-T-TAAAA is described in ClinVar as [Benign]. Clinvar id is 1252159.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CARD14	NM_001366385.1	c.-20-319_-20-316dup		intron_variant		ENST00000648509.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARD14	ENST00000648509.2	c.-20-319_-20-316dup		intron_variant			NM_001366385.1	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 28386 AN: 141004 Hom.: 2807 Cov.: 20

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 28402 AN: 141046 Hom.: 2811 Cov.: 20 AF XY: 0.197 AC XY: 13449 AN XY: 68106

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.169

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 05, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60307812; hg19: chr17-78154888;