12-57797930-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_006576.4(AVIL):c.2412G>A(p.Leu804=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000098 in 1,612,316 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00010 ( 2 hom. )
Consequence
AVIL
NM_006576.4 synonymous
NM_006576.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.10
Genes affected
AVIL (HGNC:14188): (advillin) The protein encoded by this gene is a member of the gelsolin/villin family of actin regulatory proteins. This protein has structural similarity to villin. It binds actin and may play a role in the development of neuronal cells that form ganglia. [provided by RefSeq, Jul 2008]
TSFM (HGNC:12367): (Ts translation elongation factor, mitochondrial) This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-3 syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 12-57797930-C-T is Benign according to our data. Variant chr12-57797930-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3036171.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVIL | NM_006576.4 | c.2412G>A | p.Leu804= | synonymous_variant | 20/20 | ENST00000549994.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVIL | ENST00000549994.2 | c.2412G>A | p.Leu804= | synonymous_variant | 20/20 | 4 | NM_006576.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000499 AC: 125AN: 250280Hom.: 2 AF XY: 0.000355 AC XY: 48AN XY: 135324
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GnomAD4 exome AF: 0.000100 AC: 146AN: 1460142Hom.: 2 Cov.: 30 AF XY: 0.0000771 AC XY: 56AN XY: 726434
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AVIL-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 06, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at