rs484345

chr11-105055340-G-A

Variant summary

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

The XR_001748352.2(LOC107984381):n.165-3020G>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 0.361 in 150,996 control chromosomes in the GnomAD database, including 10,737 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 0.36 (10737 hom., cov: 32)
• Consequence: LOC107984381 XR_001748352.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984381	XR_001748352.2	n.165-3020G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARD16	ENST00000525374.1	n.25-10682C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54450 AN: 150880 Hom.: 10729 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.361 AC: 54493 AN: 150996 Hom.: 10737 Cov.: 32 AF XY: 0.363 AC XY: 26763 AN XY: 73780

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.391

Alfa AF: 0.343 Hom.: 1201

Bravo AF: 0.367

Asia WGS AF: 0.538 AC: 1874 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.3
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484345; hg19: chr11-104926067;