11-105055340-G-A

Variant names:

• chr11-105055340-G-A
• rs484345
• ENST00000525374.1:n.25-10682C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525374.1(CARD16):​n.25-10682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 150,996 control chromosomes in the GnomAD database, including 10,737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10737 hom., cov: 32)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 4 publications found

Genes affected

CARD16 (HGNC:33701): (caspase recruitment domain family member 16) Enables several functions, including CARD domain binding activity; cysteine-type endopeptidase inhibitor activity; and enzyme binding activity. Involved in several processes, including negative regulation of cysteine-type endopeptidase activity; regulation of gene expression; and regulation of signal transduction. Part of protease inhibitor complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303891 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525374.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	ENST00000525374.1	TSL:3	n.25-10682C>T		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-3020G>A		intron	N/A
	ENSG00000288255	ENST00000672013.1		n.*227C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54450 AN: 150880 Hom.: 10729 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.361 AC: 54493 AN: 150996 Hom.: 10737 Cov.: 32 AF XY: 0.363 AC XY: 26763 AN XY: 73780

African (AFR) AF: 0.332 AC: 13465 AN: 40532

American (AMR) AF: 0.401 AC: 6099 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3158 AN: 5160

South Asian (SAS) AF: 0.570 AC: 2744 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2800 AN: 10530

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23314 AN: 67958

Other (OTH) AF: 0.391 AC: 821 AN: 2098

Alfa AF: 0.342 Hom.: 1237

Bravo AF: 0.367

Asia WGS AF: 0.538 AC: 1874 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs484345; hg19: chr11-104926067;