rs840385
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_181435.6(C1QTNF3):c.*330A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
C1QTNF3
NM_181435.6 3_prime_UTR
NM_181435.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0350
Genes affected
C1QTNF3 (HGNC:14326): (C1q and TNF related 3) Enables identical protein binding activity. Involved in several processes, including cellular triglyceride homeostasis; negative regulation of NIK/NF-kappaB signaling; and regulation of cytokine production. Acts upstream of or within negative regulation of gluconeogenesis. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF3 | NM_181435.6 | c.*330A>T | 3_prime_UTR_variant | 6/6 | ENST00000382065.8 | ||
C1QTNF3-AMACR | NR_037951.1 | n.764+334A>T | intron_variant, non_coding_transcript_variant | ||||
C1QTNF3 | NM_030945.4 | c.*330A>T | 3_prime_UTR_variant | 6/6 | |||
C1QTNF3 | NR_146599.1 | n.1881A>T | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF3 | ENST00000382065.8 | c.*330A>T | 3_prime_UTR_variant | 6/6 | 1 | NM_181435.6 | P4 | ||
C1QTNF3 | ENST00000231338.7 | c.*330A>T | 3_prime_UTR_variant | 6/6 | 1 | A1 | |||
C1QTNF3 | ENST00000513471.5 | n.845A>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
C1QTNF3 | ENST00000508398.1 | n.1000A>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 54862Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 28652
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
54862
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
28652
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at