20-38354288-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004139.5(LBP):c.373C>A(p.Leu125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,612,580 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004139.5 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 |
---|---|---|---|---|---|---|---|
LBP | NM_004139.5 | c.373C>A | p.Leu125Ile | missense_variant | 4/15 | ENST00000217407.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LBP | ENST00000217407.3 | c.373C>A | p.Leu125Ile | missense_variant | 4/15 | 1 | NM_004139.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00493 AC: 750AN: 152190Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00788 AC: 1971AN: 249978Hom.: 41 AF XY: 0.00643 AC XY: 869AN XY: 135152
GnomAD4 exome AF: 0.00378 AC: 5524AN: 1460272Hom.: 66 Cov.: 30 AF XY: 0.00349 AC XY: 2532AN XY: 726436
GnomAD4 genome AF: 0.00495 AC: 754AN: 152308Hom.: 7 Cov.: 32 AF XY: 0.00543 AC XY: 404AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at