11-62338055-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001083926.2(ASRGL1):c.78C>T(p.Gly26=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
ASRGL1
NM_001083926.2 synonymous
NM_001083926.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.10
Genes affected
ASRGL1 (HGNC:16448): (asparaginase and isoaspartyl peptidase 1) Enables asparaginase activity and beta-aspartyl-peptidase activity. Involved in asparagine catabolic process via L-aspartate. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP7
Synonymous conserved (PhyloP=-1.1 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ASRGL1 | NM_001083926.2 | c.78C>T | p.Gly26= | synonymous_variant | 2/7 | ENST00000415229.6 | NP_001077395.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ASRGL1 | ENST00000415229.6 | c.78C>T | p.Gly26= | synonymous_variant | 2/7 | 1 | NM_001083926.2 | ENSP00000400057 | P1 | |
| ENST00000400902.4 | n.36G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455806Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723766
GnomAD4 exome
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1455806
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32
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0
AN XY:
723766
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GnomAD4 genome
GnomAD4 genome
Cov.:
34
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 | Labcorp Genetics (formerly Invitae), Labcorp | Feb 05, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 1025801). This variant has not been reported in the literature in individuals affected with ASRGL1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 26 of the ASRGL1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ASRGL1 protein. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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