17-80181089-TA-T

Variant names:

• chr17-80181089-TA-T
• rs60307812
• NM_001366385.1:c.-20-316delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.511
• Publications: 0 publications found

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]

CARD14 Gene-Disease associations (from GenCC):

• familial pityriasis rubra pilaris

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, Orphanet
• psoriasis 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366385.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD14	NM_001366385.1	MANE Select	c.-20-316delA		intron	N/A	NP_001353314.1	Q9BXL6-1
	CARD14	NM_024110.4		c.-20-316delA		intron	N/A	NP_077015.2	Q9BXL6-1
	CARD14	NM_001257970.1		c.-20-316delA		intron	N/A	NP_001244899.1	Q9BXL6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD14	ENST00000648509.2	MANE Select	c.-20-329delA		intron	N/A	ENSP00000498071.1	Q9BXL6-1
	CARD14	ENST00000344227.6	TSL:1	c.-20-329delA		intron	N/A	ENSP00000344549.2	Q9BXL6-1
	CARD14	ENST00000570421.5	TSL:1	c.-20-329delA		intron	N/A	ENSP00000461806.1	Q9BXL6-2

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 4832 AN: 141168 Hom.: 205 Cov.: 20

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

African (AFR) AF: 0.108 AC: 4171 AN: 38750

American (AMR) AF: 0.0208 AC: 292 AN: 14066

Ashkenazi Jewish (ASJ) AF: 0.0174 AC: 58 AN: 3326

East Asian (EAS) AF: 0.00185 AC: 9 AN: 4864

South Asian (SAS) AF: 0.00293 AC: 13 AN: 4438

European-Finnish (FIN) AF: 0.00624 AC: 52 AN: 8328

Middle Eastern (MID) AF: 0.0216 AC: 6 AN: 278

European-Non Finnish (NFE) AF: 0.00286 AC: 184 AN: 64354

Other (OTH) AF: 0.0262 AC: 51 AN: 1944

Alfa AF: 0.000182 Hom.: 106

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs60307812; hg19: chr17-78154888; COSMIC: COSV60125913; COSMIC: COSV60125913;