18-67511043-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032160.3(DSEL):āc.3566A>Gā(p.Asp1189Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000103 in 1,461,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.000010 ( 0 hom. )
Consequence
DSEL
NM_032160.3 missense
NM_032160.3 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
DSEL (HGNC:18144): (dermatan sulfate epimerase like) Predicted to enable chondroitin-glucuronate 5-epimerase activity. Predicted to be involved in chondroitin sulfate metabolic process and dermatan sulfate metabolic process. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09344721).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DSEL | NM_032160.3 | c.3566A>G | p.Asp1189Gly | missense_variant | 2/2 | ENST00000310045.9 | NP_115536.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DSEL | ENST00000310045.9 | c.3566A>G | p.Asp1189Gly | missense_variant | 2/2 | 2 | NM_032160.3 | ENSP00000310565.8 | ||
ENSG00000263424 | ENST00000583493.1 | n.302T>C | non_coding_transcript_exon_variant | 2/2 | 5 | |||||
ENSG00000263424 | ENST00000581951.1 | n.308-7T>C | splice_region_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250532Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135360
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461086Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 726798
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GnomAD4 genome Cov.: 33
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33
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.3596A>G (p.D1199G) alteration is located in exon 2 (coding exon 1) of the DSEL gene. This alteration results from a A to G substitution at nucleotide position 3596, causing the aspartic acid (D) at amino acid position 1199 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
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