22-19971146-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001670.3(ARVCF):c.*12+70C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 1,540,188 control chromosomes in the GnomAD database, including 336,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.55 ( 24885 hom., cov: 33)
Exomes 𝑓: 0.66 ( 312002 hom. )
Consequence
ARVCF
NM_001670.3 intron
NM_001670.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.625
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 22-19971146-G-A is Benign according to our data. Variant chr22-19971146-G-A is described in ClinVar as [Benign]. Clinvar id is 1280000.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
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.*12+70C>T | intron_variant | ENST00000263207.8 | NP_001661.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARVCF | ENST00000263207.8 | c.*12+70C>T | intron_variant | 1 | NM_001670.3 | ENSP00000263207 | P4 | |||
ARVCF | ENST00000495096.5 | n.1704-403C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.555 AC: 81732AN: 147194Hom.: 24892 Cov.: 33
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GnomAD4 exome AF: 0.664 AC: 924890AN: 1392884Hom.: 312002 AF XY: 0.662 AC XY: 454651AN XY: 687226
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GnomAD4 genome AF: 0.555 AC: 81723AN: 147304Hom.: 24885 Cov.: 33 AF XY: 0.553 AC XY: 39873AN XY: 72070
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at