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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARD14	NM_001366385.1	c.-20-316delA		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.-20-329delA		intron_variant	Intron 4 of 23		NM_001366385.1	ENSP00000498071.1

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

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 06, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

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

Publications

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Other links and lift over

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