11-66858944-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024036.5(LRFN4):c.1200G>T(p.Glu400Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000702 in 1,425,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024036.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRFN4 | NM_024036.5 | c.1200G>T | p.Glu400Asp | missense_variant | 1/2 | ENST00000309602.5 | |
PC | NM_001040716.2 | c.1368+4830C>A | intron_variant | ENST00000393960.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRFN4 | ENST00000309602.5 | c.1200G>T | p.Glu400Asp | missense_variant | 1/2 | 1 | NM_024036.5 | P1 | |
PC | ENST00000393960.7 | c.1368+4830C>A | intron_variant | 5 | NM_001040716.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.02e-7 AC: 1AN: 1425228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 704080
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at