3-69109116-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_198271.5(LMOD3):āc.1662A>Gā(p.Gln554Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,450,564 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 Likely benign (ā ).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
LMOD3
NM_198271.5 synonymous
NM_198271.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.349
Genes affected
LMOD3 (HGNC:6649): (leiomodin 3) The protein encoded by this gene is a member of the leiomodin family of proteins. This protein contains three actin-binding domains, a tropomyosin domain, a leucine-rich repeat domain, and a Wiskott-Aldrich syndrome protein homology 2 domain (WH2). Localization of this protein to the pointed ends of thin filaments has been observed, and there is evidence that this protein acts as a catalyst of actin nucleation, and is important to the organization of sarcomeric thin filaments in skeletal muscles. Mutations in this gene have been associated as one cause of Nemaline myopathy, as other genes have also been linked to this disorder. Nemaline myopathy is a disorder characterized by nonprogressive generalized muscle weakness and protein inclusions (nemaline bodies) in skeletal myofibers. Patients with mutations in this gene often present with a severe congenital form of the disorder. [provided by RefSeq, Jan 2015]
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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;
BP6
Variant 3-69109116-T-C is Benign according to our data. Variant chr3-69109116-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3704740.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1662A>G | p.Gln554Gln | synonymous_variant | Exon 3 of 3 | 1 | NM_198271.5 | ENSP00000414670.3 | ||
LMOD3 | ENST00000475434.1 | c.1662A>G | p.Gln554Gln | synonymous_variant | Exon 4 of 4 | 5 | ENSP00000418645.1 | |||
LMOD3 | ENST00000489031.5 | c.1662A>G | p.Gln554Gln | synonymous_variant | Exon 4 of 4 | 2 | ENSP00000417210.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
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31
GnomAD3 exomes AF: 0.00000439 AC: 1AN: 227782Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123050
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GnomAD4 exome AF: 0.00000138 AC: 2AN: 1450564Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 720240
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GnomAD4 genome Cov.: 31
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Nemaline myopathy 10 Benign:1
Dec 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at