chr17-80181089-T-TA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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
• 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

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
CARD14	NM_001366385.1	c.-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
CARD14	ENST00000648509.2	c.-20-330_-20-329insA		intron_variant	Intron 4 of 23		NM_001366385.1	ENSP00000498071.1

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4292 AN: 141346 Hom.: 76 Cov.: 20

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

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

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

Other links and lift over

dbSNP: rs60307812; hg19: chr17-78154888;