3-134603672-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_178554.6(KY):āc.1893A>Gā(p.Thr631Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 1,613,802 control chromosomes in the GnomAD database, including 849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.039 ( 421 hom., cov: 33)
Exomes š: 0.0044 ( 428 hom. )
Consequence
KY
NM_178554.6 synonymous
NM_178554.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.07
Genes affected
KY (HGNC:26576): (kyphoscoliosis peptidase) The protein encoded by this gene belongs to the transglutaminase-like superfamily. The protein is involved in the function, maturation and stabilization of the neuromuscular junction and may be required for normal muscle growth. Mutations in this gene are associated with myopathy, myofibrillar, 7. [provided by RefSeq, Apr 2017]
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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=-0.89).
BP6
Variant 3-134603672-T-C is Benign according to our data. Variant chr3-134603672-T-C is described in ClinVar as [Benign]. Clinvar id is 1244064.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.07 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KY | NM_178554.6 | c.1893A>G | p.Thr631Thr | synonymous_variant | 11/11 | ENST00000423778.7 | NP_848649.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KY | ENST00000423778.7 | c.1893A>G | p.Thr631Thr | synonymous_variant | 11/11 | 5 | NM_178554.6 | ENSP00000397598.2 |
Frequencies
GnomAD3 genomes AF: 0.0394 AC: 5994AN: 152214Hom.: 420 Cov.: 33
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GnomAD3 exomes AF: 0.0104 AC: 2578AN: 249028Hom.: 175 AF XY: 0.00771 AC XY: 1042AN XY: 135078
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GnomAD4 exome AF: 0.00436 AC: 6365AN: 1461470Hom.: 428 Cov.: 30 AF XY: 0.00374 AC XY: 2717AN XY: 726988
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GnomAD4 genome AF: 0.0394 AC: 6002AN: 152332Hom.: 421 Cov.: 33 AF XY: 0.0385 AC XY: 2869AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2021 | - - |
Computational scores
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at