chr6-69676224-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_018368.4(LMBRD1):c.1557G>A(p.Ser519=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,461,126 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. S519S) has been classified as Likely benign.
Frequency
Consequence
NM_018368.4 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 |
---|---|---|---|---|---|---|---|
LMBRD1 | NM_018368.4 | c.1557G>A | p.Ser519= | synonymous_variant | 16/16 | ENST00000649934.3 | |
LMBRD1 | NM_001363722.2 | c.1338G>A | p.Ser446= | synonymous_variant | 16/16 | ||
LMBRD1 | NM_001367271.1 | c.1338G>A | p.Ser446= | synonymous_variant | 16/16 | ||
LMBRD1 | NM_001367272.1 | c.1338G>A | p.Ser446= | synonymous_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMBRD1 | ENST00000649934.3 | c.1557G>A | p.Ser519= | synonymous_variant | 16/16 | NM_018368.4 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250712Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135486
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461126Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 726844
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Methylmalonic aciduria and homocystinuria type cblF Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at