chr6-106571412-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001371242.2(CRYBG1):c.*2846C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,378 control chromosomes in the GnomAD database, including 2,477 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2476 hom., cov: 32)
Exomes 𝑓: 0.11 ( 1 hom. )
Consequence
CRYBG1
NM_001371242.2 3_prime_UTR
NM_001371242.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.597
Genes affected
CRYBG1 (HGNC:356): (crystallin beta-gamma domain containing 1) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]
RTN4IP1 (HGNC:18647): (reticulon 4 interacting protein 1) This gene encodes a mitochondrial protein that interacts with reticulon 4, which is a potent inhibitor of regeneration following spinal cord injury. This interaction may be important for reticulon-induced inhibition of neurite growth. Mutations in this gene can cause optic atrophy 10, with or without ataxia, cognitive disability, and seizures. There is a pseudogene for this gene on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRYBG1 | NM_001371242.2 | c.*2846C>T | 3_prime_UTR_variant | 22/22 | ENST00000633556.3 | NP_001358171.1 | ||
RTN4IP1 | NM_032730.5 | c.*584G>A | 3_prime_UTR_variant | 9/9 | ENST00000369063.8 | NP_116119.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTN4IP1 | ENST00000369063.8 | c.*584G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_032730.5 | ENSP00000358059 | P1 | ||
CRYBG1 | ENST00000633556.3 | c.*2846C>T | 3_prime_UTR_variant | 22/22 | 5 | NM_001371242.2 | ENSP00000488010 | P1 |
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24744AN: 151988Hom.: 2474 Cov.: 32
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GnomAD4 exome AF: 0.107 AC: 29AN: 272Hom.: 1 Cov.: 0 AF XY: 0.109 AC XY: 17AN XY: 156
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GnomAD4 genome AF: 0.163 AC: 24751AN: 152106Hom.: 2476 Cov.: 32 AF XY: 0.162 AC XY: 12022AN XY: 74380
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at