rs34672588
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000332972.9(ADSS1):c.6G>A(p.Val2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 787,880 control chromosomes in the GnomAD database, including 56,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.46 ( 15282 hom., cov: 26)
Exomes 𝑓: 0.25 ( 41001 hom. )
Consequence
ADSS1
ENST00000332972.9 synonymous
ENST00000332972.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.145
Genes affected
ADSS1 (HGNC:20093): (adenylosuccinate synthase 1) This gene encodes a member of the adenylosuccinate synthase family of proteins. The encoded muscle-specific enzyme plays a role in the purine nucleotide cycle by catalyzing the first step in the conversion of inosine monophosphate (IMP) to adenosine monophosphate (AMP). Mutations in this gene may cause adolescent onset distal myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 14-104729898-G-A is Benign according to our data. Variant chr14-104729898-G-A is described in ClinVar as [Benign]. Clinvar id is 1189013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADSS1 | NM_152328.5 | c.193-5122G>A | intron_variant | ENST00000330877.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADSS1 | ENST00000330877.7 | c.193-5122G>A | intron_variant | 1 | NM_152328.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.458 AC: 54114AN: 118048Hom.: 15261 Cov.: 26
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GnomAD3 exomes AF: 0.311 AC: 21025AN: 67694Hom.: 6156 AF XY: 0.300 AC XY: 10537AN XY: 35104
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GnomAD4 exome AF: 0.253 AC: 169475AN: 669770Hom.: 41001 Cov.: 17 AF XY: 0.266 AC XY: 89409AN XY: 336586
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GnomAD4 genome ? AF: 0.459 AC: 54155AN: 118110Hom.: 15282 Cov.: 26 AF XY: 0.461 AC XY: 26178AN XY: 56788
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Myopathy, distal, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
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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
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at