13-24316068-C-T

Variant summary

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

The NM_178540.5(C1QTNF9):​c.65C>T​(p.Thr22Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T22N) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

C1QTNF9
NM_178540.5 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.658
Variant links:
Genes affected
C1QTNF9 (HGNC:28732): (C1q and TNF related 9) Enables identical protein binding activity. Predicted to be involved in signal transduction. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]
C1QTNF9-AS1 (HGNC:39906): (C1QTNF9 antisense RNA 1)

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=0.0882127).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C1QTNF9NM_178540.5 linkc.65C>T p.Thr22Ile missense_variant Exon 2 of 4 ENST00000332018.5 NP_848635.2 P0C862A0A3B0J259
C1QTNF9NM_001303137.2 linkc.65C>T p.Thr22Ile missense_variant Exon 3 of 5 NP_001290066.1 P0C862A0A3B0J259
C1QTNF9NM_001303138.2 linkc.65C>T p.Thr22Ile missense_variant Exon 2 of 4 NP_001290067.1 P0C862A0A3B0J259

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C1QTNF9ENST00000332018.5 linkc.65C>T p.Thr22Ile missense_variant Exon 2 of 4 1 NM_178540.5 ENSP00000333737.4 P0C862
ENSG00000273167ENST00000382141.4 linkn.*61C>T non_coding_transcript_exon_variant Exon 14 of 16 5 ENSP00000371576.4 A0A0A0MRY4
ENSG00000273167ENST00000382141.4 linkn.*61C>T 3_prime_UTR_variant Exon 14 of 16 5 ENSP00000371576.4 A0A0A0MRY4

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151850
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251408
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135870
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461784
Hom.:
0
Cov.:
33
AF XY:
0.00000275
AC XY:
2
AN XY:
727204
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151850
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
74174
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
9.6
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0049
T;T
Eigen
Benign
-0.56
Eigen_PC
Benign
-0.54
FATHMM_MKL
Benign
0.17
N
LIST_S2
Benign
0.41
.;T
M_CAP
Benign
0.050
D
MetaRNN
Benign
0.088
T;T
MetaSVM
Benign
-0.48
T
MutationAssessor
Uncertain
2.0
M;M
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.80
N;N
REVEL
Benign
0.19
Sift
Benign
0.13
T;T
Sift4G
Benign
0.19
T;T
Polyphen
0.0010
B;B
Vest4
0.10
MutPred
0.43
Gain of catalytic residue at R24 (P = 0.0107);Gain of catalytic residue at R24 (P = 0.0107);
MVP
0.67
ClinPred
0.082
T
GERP RS
1.9
Varity_R
0.067
gMVP
0.18

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1487669623; hg19: chr13-24890206; API