15-45043286-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_003104.6(SORD):āc.130A>Gā(p.Ile44Val) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000045 ( 0 hom., cov: 20)
Exomes š: 0.000043 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SORD
NM_003104.6 missense
NM_003104.6 missense
Scores
4
6
9
Clinical Significance
Conservation
PhyloP100: 9.23
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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORD | NM_003104.6 | c.130A>G | p.Ile44Val | missense_variant | 3/9 | ENST00000267814.14 | |
SORD | NR_034039.2 | n.219A>G | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORD | ENST00000267814.14 | c.130A>G | p.Ile44Val | missense_variant | 3/9 | 1 | NM_003104.6 | P1 | |
ENST00000560324.1 | n.324-798T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 6AN: 132720Hom.: 0 Cov.: 20 FAILED QC
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000553 AC: 9AN: 162788Hom.: 0 AF XY: 0.0000458 AC XY: 4AN XY: 87266
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000434 AC: 26AN: 598864Hom.: 0 Cov.: 6 AF XY: 0.0000433 AC XY: 14AN XY: 323406
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000452 AC: 6AN: 132720Hom.: 0 Cov.: 20 AF XY: 0.0000314 AC XY: 2AN XY: 63662
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | SORD: PP2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at