chr5-38523528-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001127671.2(LIFR):c.452C>G(p.Ser151Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000408 in 1,613,098 control chromosomes in the GnomAD database, including 2 homozygotes. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001127671.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIFR | ENST00000453190.7 | c.452C>G | p.Ser151Cys | missense_variant | Exon 5 of 20 | 2 | NM_001127671.2 | ENSP00000398368.2 | ||
LIFR | ENST00000263409.8 | c.452C>G | p.Ser151Cys | missense_variant | Exon 5 of 20 | 1 | ENSP00000263409.4 | |||
LIFR | ENST00000503088.1 | n.615C>G | non_coding_transcript_exon_variant | Exon 5 of 15 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251086Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135764
GnomAD4 exome AF: 0.000435 AC: 636AN: 1460912Hom.: 2 Cov.: 30 AF XY: 0.000422 AC XY: 307AN XY: 726830
GnomAD4 genome AF: 0.000145 AC: 22AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74338
ClinVar
Submissions by phenotype
not provided Uncertain:2
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This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 151 of the LIFR protein (p.Ser151Cys). This variant is present in population databases (rs61751712, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with LIFR-related conditions. ClinVar contains an entry for this variant (Variation ID: 501917). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Stüve-Wiedemann syndrome 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at