chr5-34020172-C-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181435.6(C1QTNF3):c.*411G>T 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
C1QTNF3
NM_181435.6 3_prime_UTR
NM_181435.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.232
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF3 | NM_181435.6 | c.*411G>T | 3_prime_UTR_variant | 6/6 | ENST00000382065.8 | ||
C1QTNF3-AMACR | NR_037951.1 | n.764+415G>T | intron_variant, non_coding_transcript_variant | ||||
C1QTNF3 | NM_030945.4 | c.*411G>T | 3_prime_UTR_variant | 6/6 | |||
C1QTNF3 | NR_146599.1 | n.1962G>T | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF3 | ENST00000382065.8 | c.*411G>T | 3_prime_UTR_variant | 6/6 | 1 | NM_181435.6 | P4 | ||
C1QTNF3 | ENST00000231338.7 | c.*411G>T | 3_prime_UTR_variant | 6/6 | 1 | A1 | |||
C1QTNF3 | ENST00000513471.5 | n.926G>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
C1QTNF3 | ENST00000508398.1 | n.1081G>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
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