chr3-69122187-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_198271.5(LMOD3):āc.200A>Gā(p.Asn67Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000156 in 1,613,456 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. N67N) has been classified as Likely benign.
Frequency
Consequence
NM_198271.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.200A>G | p.Asn67Ser | missense_variant | 1/3 | ENST00000420581.7 | |
LMOD3 | NM_001304418.3 | c.200A>G | p.Asn67Ser | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.200A>G | p.Asn67Ser | missense_variant | 1/3 | 1 | NM_198271.5 | P1 | |
LMOD3 | ENST00000475434.1 | c.200A>G | p.Asn67Ser | missense_variant | 2/4 | 5 | P1 | ||
LMOD3 | ENST00000489031.5 | c.200A>G | p.Asn67Ser | missense_variant | 2/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000299 AC: 74AN: 247846Hom.: 0 AF XY: 0.000424 AC XY: 57AN XY: 134480
GnomAD4 exome AF: 0.000162 AC: 237AN: 1461164Hom.: 5 Cov.: 32 AF XY: 0.000224 AC XY: 163AN XY: 726826
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74474
ClinVar
Submissions by phenotype
Nemaline myopathy 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at