11-105053224-G-T

Variant names:

• chr11-105053224-G-T
• rs508760
• ENST00000525374.1:n.25-8566C>A

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-8566C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,438 control chromosomes in the GnomAD database, including 1,310 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 0.10 (1310 hom., cov: 33)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	ENST00000525374.1	TSL:3	n.25-8566C>A		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-5136G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15461 AN: 151320 Hom.: 1304 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0742

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.102 AC: 15479 AN: 151438 Hom.: 1310 Cov.: 33 AF XY: 0.100 AC XY: 7423 AN XY: 74026

African (AFR) AF: 0.163 AC: 6634 AN: 40780

American (AMR) AF: 0.0837 AC: 1277 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3472

East Asian (EAS) AF: 0.156 AC: 807 AN: 5170

South Asian (SAS) AF: 0.140 AC: 674 AN: 4828

European-Finnish (FIN) AF: 0.0286 AC: 304 AN: 10616

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5048 AN: 68018

Other (OTH) AF: 0.106 AC: 222 AN: 2094

Alfa AF: 0.0830 Hom.: 688

Bravo AF: 0.110

Asia WGS AF: 0.175 AC: 608 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.094
DANN	Benign	0.64
PhyloP100		-1.5
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: rs508760; hg19: chr11-104923951;