chr3-69109098-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_198271.5(LMOD3):c.1680G>A(p.Ala560=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,600,726 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 (★). Synonymous variant affecting the same amino acid position (i.e. A560A) has been classified as Likely benign.
Frequency
Consequence
NM_198271.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.1680G>A | p.Ala560= | synonymous_variant | 3/3 | ENST00000420581.7 | |
LMOD3 | NM_001304418.3 | c.1680G>A | p.Ala560= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1680G>A | p.Ala560= | synonymous_variant | 3/3 | 1 | NM_198271.5 | P1 | |
LMOD3 | ENST00000475434.1 | c.1680G>A | p.Ala560= | synonymous_variant | 4/4 | 5 | P1 | ||
LMOD3 | ENST00000489031.5 | c.1680G>A | p.Ala560= | synonymous_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000887 AC: 2AN: 225478Hom.: 0 AF XY: 0.00000821 AC XY: 1AN XY: 121734
GnomAD4 exome AF: 0.0000193 AC: 28AN: 1448558Hom.: 0 Cov.: 29 AF XY: 0.0000278 AC XY: 20AN XY: 719072
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74330
ClinVar
Submissions by phenotype
Nemaline myopathy 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at