rs514573

Variant names:

• chr11-105056293-T-G
• rs514573
• ENST00000525374.1:n.25-11635A>C

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-11635A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 151,124 control chromosomes in the GnomAD database, including 67,035 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 0.94 (67035 hom., cov: 31)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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.25-11635A>C		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-2067T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.935 AC: 141226 AN: 151004 Hom.: 66999 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.962

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.935 AC: 141314 AN: 151124 Hom.: 67035 Cov.: 31 AF XY: 0.936 AC XY: 69173 AN XY: 73882

African (AFR) AF: 0.790 AC: 32013 AN: 40516

American (AMR) AF: 0.966 AC: 14715 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3438 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5146 AN: 5148

South Asian (SAS) AF: 0.963 AC: 4644 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10609 AN: 10610

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67595 AN: 68018

Other (OTH) AF: 0.939 AC: 1969 AN: 2098

Alfa AF: 0.955 Hom.: 9046

Bravo AF: 0.927

Asia WGS AF: 0.970 AC: 3369 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.11
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: rs514573; hg19: chr11-104927020;