chr10-117134362-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001112704.2(VAX1):c.651G>C(p.Leu217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,171,396 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 0 hom. )
Consequence
VAX1
NM_001112704.2 synonymous
NM_001112704.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.783
Genes affected
VAX1 (HGNC:12660): (ventral anterior homeobox 1) This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors which are conserved in vertebrates. Genes of this family are involved in the regulation of body development and morphogenesis. The most conserved genes, called HOX genes are found in special gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play an important role in the development of anterior ventral forebrain and visual system. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 10-117134362-C-G is Benign according to our data. Variant chr10-117134362-C-G is described in ClinVar as [Benign]. Clinvar id is 2026441.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.783 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAX1 | NM_001112704.2 | c.651G>C | p.Leu217= | synonymous_variant | 3/3 | ENST00000369206.6 | |
VAX1 | NM_199131.3 | c.430-1885G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX1 | ENST00000369206.6 | c.651G>C | p.Leu217= | synonymous_variant | 3/3 | 5 | NM_001112704.2 | P1 | |
VAX1 | ENST00000277905.6 | c.430-1885G>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 165AN: 147848Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.000276 AC: 283AN: 1023548Hom.: 0 Cov.: 32 AF XY: 0.000250 AC XY: 121AN XY: 483228
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GnomAD4 genome ? AF: 0.00112 AC: 165AN: 147848Hom.: 1 Cov.: 32 AF XY: 0.00186 AC XY: 134AN XY: 71956
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Microphthalmia, syndromic 11 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at