rs1699087

Positions:

• chr11-105059346-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001748352.2(LOC107984381):​n.218+933C>A variant causes a intron, non coding transcript 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: LOC107984381 XR_001748352.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

Genes affected

LOC107984381 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107984381	XR_001748352.2	n.218+933C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARD16	ENST00000525374.1	n.25-14688G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.442

Alfa AF: 0.519 Hom.: 2745

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1699087; hg19: chr11-104930073;