chr5-38485873-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_001127671.2(LIFR):āc.2443A>Gā(p.Thr815Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T815R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001127671.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIFR | NM_001127671.2 | c.2443A>G | p.Thr815Ala | missense_variant | 17/20 | ENST00000453190.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIFR | ENST00000453190.7 | c.2443A>G | p.Thr815Ala | missense_variant | 17/20 | 2 | NM_001127671.2 | P1 | |
LIFR | ENST00000263409.8 | c.2443A>G | p.Thr815Ala | missense_variant | 17/20 | 1 | P1 | ||
LIFR | ENST00000508477.5 | n.276A>G | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251452Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Stuve-Wiedemann syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 01, 2017 | Likely pathogenicity based on finding it once in our laboratory in trans with a nonsense variant in a 16-year-old male with congenital muscular dystrophy, scoliosis, spasticity, febrile seizures, dysmorphism, short stature, joint contractures, nasal speech, mild dysarthria - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at