6-106571786-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001371242.2(CRYBG1):c.*3220T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 481,260 control chromosomes in the GnomAD database, including 4,695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2438 hom., cov: 33)
Exomes 𝑓: 0.11 ( 2257 hom. )
Consequence
CRYBG1
NM_001371242.2 3_prime_UTR
NM_001371242.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.94
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 6-106571786-T-C is Benign according to our data. Variant chr6-106571786-T-C is described in ClinVar as [Benign]. Clinvar id is 1238463.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYBG1 | NM_001371242.2 | c.*3220T>C | 3_prime_UTR_variant | 22/22 | ENST00000633556.3 | ||
RTN4IP1 | NM_032730.5 | c.*210A>G | 3_prime_UTR_variant | 9/9 | ENST00000369063.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTN4IP1 | ENST00000369063.8 | c.*210A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_032730.5 | P1 | ||
CRYBG1 | ENST00000633556.3 | c.*3220T>C | 3_prime_UTR_variant | 22/22 | 5 | NM_001371242.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24717AN: 151962Hom.: 2436 Cov.: 33
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GnomAD4 exome AF: 0.108 AC: 35625AN: 329180Hom.: 2257 Cov.: 3 AF XY: 0.109 AC XY: 18901AN XY: 174190
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GnomAD4 genome AF: 0.163 AC: 24724AN: 152080Hom.: 2438 Cov.: 33 AF XY: 0.161 AC XY: 11987AN XY: 74330
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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 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at