rs1785882

Variant names:

• chr11-105052348-A-T
• rs1785882
• ENST00000525374.1:n.25-7690T>A

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-7690T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,100 control chromosomes in the GnomAD database, including 16,899 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 0.45 (16899 hom., cov: 33)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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.25-7690T>A		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-6012A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68827 AN: 151982 Hom.: 16893 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.453 AC: 68840 AN: 152100 Hom.: 16899 Cov.: 33 AF XY: 0.449 AC XY: 33412 AN XY: 74352

African (AFR) AF: 0.290 AC: 12024 AN: 41500

American (AMR) AF: 0.354 AC: 5410 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1982 AN: 5176

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4824

European-Finnish (FIN) AF: 0.608 AC: 6418 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38586 AN: 67980

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.511 Hom.: 2621

Bravo AF: 0.429

Asia WGS AF: 0.365 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		0.21
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: rs1785882; hg19: chr11-104923075;