rs1864115943

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_052889.4(CARD16):​c.*61G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,504 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

CARD16
NM_052889.4 3_prime_UTR

Scores

5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.300
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19219232).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CARD16NM_052889.4 linkc.*61G>T 3_prime_UTR_variant Exon 4 of 4 ENST00000673097.2 NP_443121.1 Q5EG05-2
CARD16NM_001394580.1 linkc.*61G>T 3_prime_UTR_variant Exon 4 of 4 NP_001381509.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CARD16ENST00000673097 linkc.*61G>T 3_prime_UTR_variant Exon 4 of 4 NM_052889.4 ENSP00000509408.1 Q5EG05-2
CARD16ENST00000672037.1 linkc.292G>T p.Asp98Tyr missense_variant Exon 3 of 3 ENSP00000509530.1 Q5EG05-1
CARD16ENST00000528513.1 linkc.244G>T p.Asp82Tyr missense_variant Exon 3 of 3 3 ENSP00000510629.1 A0A8I5KS59
CARD16ENST00000525374.1 linkn.372G>T non_coding_transcript_exon_variant Exon 4 of 4 3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461504
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
727046
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.085
T
BayesDel_noAF
Benign
-0.36
CADD
Benign
7.8
DANN
Uncertain
0.98
DEOGEN2
Benign
0.067
T;.
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.55
FATHMM_MKL
Benign
0.032
N
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.0023
T
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.0
M;.
PROVEAN
Uncertain
-2.8
D;D
REVEL
Benign
0.091
Sift
Uncertain
0.0030
D;D
Sift4G
Uncertain
0.0020
D;.
Polyphen
1.0
D;.
Vest4
0.31
MutPred
0.50
Gain of catalytic residue at D98 (P = 0.0127);.;
MVP
0.34
MPC
0.81
ClinPred
0.86
D
GERP RS
1.4
Varity_R
0.27
gMVP
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-104912429; API