chr11-105041702-C-G

Variant names:

• chr11-105041702-C-G
• rs1864115943
• NM_052889.4:c.*61G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_052889.4(CARD16):​c.*61G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CARD16 NM_052889.4 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.300
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15627638).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052889.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	NM_052889.4	MANE Select	c.*61G>C		3_prime_UTR	Exon 4 of 4	NP_443121.1	Q5EG05-2
	CARD16	NM_001394580.1		c.*61G>C		3_prime_UTR	Exon 4 of 4	NP_001381509.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	ENST00000673097.2	MANE Select	c.*61G>C		3_prime_UTR	Exon 4 of 4	ENSP00000509408.1	Q5EG05-2
	CARD16	ENST00000672037.2		c.292G>C	p.Asp98His	missense	Exon 3 of 3	ENSP00000509530.1	Q5EG05-1
	CARD16	ENST00000528513.1	TSL:3	c.244G>C	p.Asp82His	missense	Exon 3 of 3	ENSP00000510629.1	A0A8I5KS59

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	6.8
DANN	Uncertain	0.98
DEOGEN2	Benign	0.011	T
Eigen	Benign	-0.29
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.047	N
LIST_S2	Benign	0.78	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.0	M
PhyloP100		0.30
PROVEAN	Benign	-2.2	N
REVEL	Benign	0.073
Sift	Uncertain	0.0080	D
Sift4G	Uncertain	0.0040	D
Polyphen		1.0	D
Vest4		0.18
MutPred		0.35		Gain of catalytic residue at N99 (P = 0.0868)
MVP		0.38
MPC		0.81
ClinPred		0.54	D
GERP RS		1.4
Varity_R		0.17
gMVP		0.14
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1864115943; hg19: chr11-104912429;