9-34370967-C-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_020702.5(MYORG):c.1977G>C(p.Thr659Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000731 in 1,613,578 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00062 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00074 ( 3 hom. )
Consequence
MYORG
NM_020702.5 synonymous
NM_020702.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.382
Genes affected
MYORG (HGNC:19918): (myogenesis regulating glycosidase (putative)) Predicted to enable hydrolase activity, hydrolyzing O-glycosyl compounds. Involved in skeletal muscle fiber development. Predicted to be located in endoplasmic reticulum membrane and nuclear membrane. Implicated in basal ganglia calcification. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 9-34370967-C-G is Benign according to our data. Variant chr9-34370967-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1681283.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.382 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000624 (95/152348) while in subpopulation AMR AF= 0.00196 (30/15304). AF 95% confidence interval is 0.00141. There are 0 homozygotes in gnomad4. There are 52 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYORG | NM_020702.5 | c.1977G>C | p.Thr659Thr | synonymous_variant | Exon 2 of 2 | ENST00000297625.8 | NP_065753.2 | |
MYORG | XM_011517966.4 | c.1977G>C | p.Thr659Thr | synonymous_variant | Exon 2 of 2 | XP_011516268.1 | ||
MYORG | XM_017014930.3 | c.1977G>C | p.Thr659Thr | synonymous_variant | Exon 2 of 2 | XP_016870419.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000624 AC: 95AN: 152230Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000600 AC: 149AN: 248502Hom.: 0 AF XY: 0.000614 AC XY: 83AN XY: 135078
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GnomAD4 exome AF: 0.000743 AC: 1085AN: 1461230Hom.: 3 Cov.: 40 AF XY: 0.000729 AC XY: 530AN XY: 726918
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GnomAD4 genome AF: 0.000624 AC: 95AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.000698 AC XY: 52AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jan 07, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at