13-20138587-CT-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_021954.4(GJA3):c.*3393del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 146,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000041 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GJA3
NM_021954.4 3_prime_UTR
NM_021954.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.21
Genes affected
GJA3 (HGNC:4277): (gap junction protein alpha 3) The protein encoded by this gene is a connexin and is a component of lens fiber gap junctions. Defects in this gene are a cause of zonular pulverulent cataract type 3 (CZP3). [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000041 (6/146276) while in subpopulation EAS AF= 0.00133 (6/4518). AF 95% confidence interval is 0.000578. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJA3 | NM_021954.4 | c.*3393del | 3_prime_UTR_variant | 2/2 | ENST00000241125.4 | ||
GJA3 | XM_011535048.3 | c.*3393del | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA3 | ENST00000241125.4 | c.*3393del | 3_prime_UTR_variant | 2/2 | 3 | NM_021954.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000411 AC: 6AN: 146148Hom.: 0 Cov.: 32
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?
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
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GnomAD4 genome ? AF: 0.0000410 AC: 6AN: 146276Hom.: 0 Cov.: 32 AF XY: 0.0000421 AC XY: 3AN XY: 71312
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Zonular Pulverulent Cataract Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at