chr13-20414254-T-TG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015974.3(CRYL1):c.634-868_634-867insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 149,568 control chromosomes in the GnomAD database, including 231 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 231 hom., cov: 30)
Consequence
CRYL1
NM_015974.3 intron
NM_015974.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.32
Genes affected
CRYL1 (HGNC:18246): (crystallin lambda 1) The uronate cycle functions as an alternative glucose metabolic pathway, accounting for about 5% of daily glucose catabolism. The product of this gene catalyzes the dehydrogenation of L-gulonate into dehydro-L-gulonate in the uronate cycle. The enzyme requires NAD(H) as a coenzyme, and is inhibited by inorganic phosphate. A similar gene in the rabbit is thought to serve a structural role in the lens of the eye. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 13-20414254-T-TG is Benign according to our data. Variant chr13-20414254-T-TG is described in ClinVar as [Benign]. Clinvar id is 1276026.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYL1 | NM_015974.3 | c.634-868_634-867insC | intron_variant | ENST00000298248.12 | |||
CRYL1 | NM_001363647.2 | c.472-868_472-867insC | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRYL1 | ENST00000298248.12 | c.634-868_634-867insC | intron_variant | 1 | NM_015974.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0339 AC: 5060AN: 149462Hom.: 231 Cov.: 30
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GnomAD4 genome ? AF: 0.0339 AC: 5076AN: 149568Hom.: 231 Cov.: 30 AF XY: 0.0351 AC XY: 2569AN XY: 73104
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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 11, 2021 | - - |
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