chr1-147907897-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005267.5(GJA8):c.-11-48G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0363 in 1,301,272 control chromosomes in the GnomAD database, including 1,099 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 83 hom., cov: 32)
Exomes 𝑓: 0.037 ( 1016 hom. )
Consequence
GJA8
NM_005267.5 intron
NM_005267.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.210
Genes affected
GJA8 (HGNC:4281): (gap junction protein alpha 8) This gene encodes a transmembrane connexin protein that is necessary for lens growth and maturation of lens fiber cells. The encoded protein is a component of gap junction channels and functions in a calcium and pH-dependent manner. Mutations in this gene have been associated with zonular pulverulent cataracts, nuclear progressive cataracts, and cataract-microcornea syndrome. [provided by RefSeq, Dec 2009]
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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 1-147907897-G-T is Benign according to our data. Variant chr1-147907897-G-T is described in ClinVar as [Benign]. Clinvar id is 1273241.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0291 (4425/152200) while in subpopulation NFE AF= 0.0457 (3111/68010). AF 95% confidence interval is 0.0444. There are 83 homozygotes in gnomad4. There are 2153 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 83 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJA8 | NM_005267.5 | c.-11-48G>T | intron_variant | ENST00000369235.2 | |||
GJA8 | XM_011509417.3 | c.-59G>T | 5_prime_UTR_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA8 | ENST00000369235.2 | c.-11-48G>T | intron_variant | NM_005267.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0291 AC: 4425AN: 152082Hom.: 83 Cov.: 32
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GnomAD4 exome AF: 0.0373 AC: 42864AN: 1149072Hom.: 1016 AF XY: 0.0364 AC XY: 21330AN XY: 585972
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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 | Oct 09, 2018 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at