rs1699087

Variant names:

• chr11-105059346-C-A
• rs1699087
• ENST00000525374.1:n.25-14688G>T

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-14688G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 150,460 control chromosomes in the GnomAD database, including 17,950 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 0.46 (17950 hom., cov: 30)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984381	XR_001748352.2	n.218+933C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARD16	ENST00000525374.1	n.25-14688G>T		intron_variant	Intron 1 of 3	3
ENSG00000303891	ENST00000797905.1	n.799+933C>A		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.465 AC: 69851 AN: 150350 Hom.: 17945 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.464 AC: 69862 AN: 150460 Hom.: 17950 Cov.: 30 AF XY: 0.460 AC XY: 33806 AN XY: 73496

African (AFR) AF: 0.312 AC: 12548 AN: 40278

American (AMR) AF: 0.359 AC: 5430 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1535 AN: 3458

East Asian (EAS) AF: 0.383 AC: 1958 AN: 5116

South Asian (SAS) AF: 0.301 AC: 1447 AN: 4806

European-Finnish (FIN) AF: 0.611 AC: 6396 AN: 10474

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39090 AN: 67884

Other (OTH) AF: 0.442 AC: 926 AN: 2096

Alfa AF: 0.511 Hom.: 2780

Bravo AF: 0.440

Asia WGS AF: 0.365 AC: 1266 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.47
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: rs1699087; hg19: chr11-104930073;