rs229541
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001365878.1(C1QTNF6):c.-71+2325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,102 control chromosomes in the GnomAD database, including 19,317 homozygotes. 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: 𝑓 0.49 ( 19316 hom., cov: 33)
Exomes 𝑓: 0.63 ( 1 hom. )
Consequence
C1QTNF6
NM_001365878.1 intron
NM_001365878.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.01
Genes affected
C1QTNF6 (HGNC:14343): (C1q and TNF related 6) Predicted to enable identical protein binding activity. Predicted to be located in extracellular space. Predicted to be integral component of membrane. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF6 | NM_001365878.1 | c.-71+2325C>T | intron_variant | ||||
C1QTNF6 | XM_011529857.3 | c.-71+103C>T | intron_variant | ||||
C1QTNF6 | XM_024452150.2 | c.-190+103C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF6 | ENST00000467564.5 | n.224+103C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
C1QTNF6 | ENST00000470655.5 | n.2921+103C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
C1QTNF6 | ENST00000497071.1 | n.433+103C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.494 AC: 75077AN: 151976Hom.: 19288 Cov.: 33
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GnomAD4 exome AF: 0.625 AC: 5AN: 8Hom.: 1 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.494 AC: 75147AN: 152094Hom.: 19316 Cov.: 33 AF XY: 0.493 AC XY: 36636AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at