rs165655
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000263207.8(ARVCF):c.*516C>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 0.665 in 989,364 control chromosomes in the GnomAD database, including 223,951 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 0.56 ( 25851 hom., cov: 33)
Exomes 𝑓: 0.68 ( 198100 hom. )
Consequence
ARVCF
ENST00000263207.8 3_prime_UTR
ENST00000263207.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.233
Genes affected
ARVCF (HGNC:728): (ARVCF delta catenin family member) Armadillo Repeat gene deleted in Velo-Cardio-Facial syndrome (ARVCF) is a member of the catenin family. This family plays an important role in the formation of adherens junction complexes, which are thought to facilitate communication between the inside and outside environments of a cell. The ARVCF gene was isolated in the search for the genetic defect responsible for the autosomal dominant Velo-Cardio-Facial syndrome (VCFS), a relatively common human disorder with phenotypic features including cleft palate, conotruncal heart defects and facial dysmorphology. The ARVCF gene encodes a protein containing two motifs, a coiled coil domain in the N-terminus and a 10 armadillo repeat sequence in the midregion. Since these sequences can facilitate protein-protein interactions ARVCF is thought to function in a protein complex. In addition, ARVCF contains a predicted nuclear-targeting sequence suggesting that it may have a function as a nuclear protein. [provided by RefSeq, Jun 2010]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARVCF | NM_001670.3 | c.*516C>T | 3_prime_UTR_variant | 20/20 | ENST00000263207.8 | NP_001661.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARVCF | ENST00000263207.8 | c.*516C>T | 3_prime_UTR_variant | 20/20 | 1 | NM_001670.3 | ENSP00000263207 | P4 | ||
ARVCF | ENST00000495096.5 | n.2207C>T | non_coding_transcript_exon_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.560 AC: 85007AN: 151764Hom.: 25857 Cov.: 33
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GnomAD4 exome AF: 0.684 AC: 573154AN: 837482Hom.: 198100 Cov.: 71 AF XY: 0.685 AC XY: 265134AN XY: 387198
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GnomAD4 genome AF: 0.560 AC: 85004AN: 151882Hom.: 25851 Cov.: 33 AF XY: 0.558 AC XY: 41423AN XY: 74226
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ClinVar
Not reported inComputational scores
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Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at