rs1021469
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006576.4(AVIL):c.67-155C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 702,464 control chromosomes in the GnomAD database, including 43,061 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.29 ( 7025 hom., cov: 32)
Exomes 𝑓: 0.34 ( 36036 hom. )
Consequence
AVIL
NM_006576.4 intron
NM_006576.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.727
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 12-57814381-G-A is Benign according to our data. Variant chr12-57814381-G-A is described in ClinVar as [Benign]. Clinvar id is 1286130.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVIL | NM_006576.4 | c.67-155C>T | intron_variant | ENST00000549994.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVIL | ENST00000549994.2 | c.67-155C>T | intron_variant | 4 | NM_006576.4 | P1 | |||
AVIL | ENST00000257861.7 | c.67-155C>T | intron_variant | 1 | P1 | ||||
AVIL | ENST00000549851.5 | c.182-155C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.287 AC: 43600AN: 151876Hom.: 7019 Cov.: 32
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GnomAD4 exome AF: 0.345 AC: 189651AN: 550470Hom.: 36036 Cov.: 7 AF XY: 0.350 AC XY: 100509AN XY: 286768
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GnomAD4 genome ? AF: 0.287 AC: 43634AN: 151994Hom.: 7025 Cov.: 32 AF XY: 0.295 AC XY: 21911AN XY: 74292
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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