chr15-45060867-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003104.6(SORD):c.266-200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 1,157,446 control chromosomes in the GnomAD database, including 2,882 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.067 ( 382 hom., cov: 32)
Exomes 𝑓: 0.077 ( 2500 hom. )
Consequence
SORD
NM_003104.6 intron
NM_003104.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0360
Genes affected
SORD (HGNC:11184): (sorbitol dehydrogenase) Sorbitol dehydrogenase (SORD; EC 1.1.1.14) catalyzes the interconversion of polyols and their corresponding ketoses, and together with aldose reductase (ALDR1; MIM 103880), makes up the sorbitol pathway that is believed to play an important role in the development of diabetic complications (summarized by Carr and Markham, 1995 [PubMed 8535074]). The first reaction of the pathway (also called the polyol pathway) is the reduction of glucose to sorbitol by ALDR1 with NADPH as the cofactor. SORD then oxidizes the sorbitol to fructose using NAD(+) cofactor.[supplied by OMIM, Jul 2010]
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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=-0.87).
BP6
Variant 15-45060867-G-A is Benign according to our data. Variant chr15-45060867-G-A is described in ClinVar as [Benign]. Clinvar id is 1239849.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0956 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORD | NM_003104.6 | c.266-200G>A | intron_variant | ENST00000267814.14 | |||
SORD | NR_034039.2 | n.355-115G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORD | ENST00000267814.14 | c.266-200G>A | intron_variant | 1 | NM_003104.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0672 AC: 9577AN: 142594Hom.: 376 Cov.: 32
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GnomAD4 exome AF: 0.0772 AC: 78322AN: 1014754Hom.: 2500 AF XY: 0.0787 AC XY: 39516AN XY: 502180
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GnomAD4 genome AF: 0.0673 AC: 9600AN: 142692Hom.: 382 Cov.: 32 AF XY: 0.0686 AC XY: 4796AN XY: 69868
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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 16, 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