11-105046918-T-C

Variant names:

• chr11-105046918-T-C
• rs11821722
• ENST00000525374.1:n.25-2260A>G

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-2260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,354 control chromosomes in the GnomAD database, including 4,696 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 0.24 (4696 hom., cov: 29)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARD16	ENST00000525374.1	n.25-2260A>G		intron_variant	Intron 1 of 3	3
ENSG00000303891	ENST00000797905.1	n.746-11442T>C		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36962 AN: 151238 Hom.: 4689 Cov.: 29

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.244 AC: 36991 AN: 151354 Hom.: 4696 Cov.: 29 AF XY: 0.242 AC XY: 17895 AN XY: 73876

African (AFR) AF: 0.216 AC: 8894 AN: 41208

American (AMR) AF: 0.196 AC: 2975 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 722 AN: 3462

East Asian (EAS) AF: 0.242 AC: 1241 AN: 5122

South Asian (SAS) AF: 0.220 AC: 1056 AN: 4794

European-Finnish (FIN) AF: 0.221 AC: 2298 AN: 10400

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19184 AN: 67858

Other (OTH) AF: 0.221 AC: 463 AN: 2096

Alfa AF: 0.266 Hom.: 3797

Bravo AF: 0.239

Asia WGS AF: 0.265 AC: 922 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.44
PhyloP100		1.0
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: rs11821722; hg19: chr11-104917645;