3-45837991-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020347.4(LZTFL1):c.64C>T(p.Arg22Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,274 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R22H) has been classified as Uncertain significance.
Frequency
Consequence
NM_020347.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LZTFL1 | NM_020347.4 | c.64C>T | p.Arg22Cys | missense_variant | 2/10 | ENST00000296135.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LZTFL1 | ENST00000296135.11 | c.64C>T | p.Arg22Cys | missense_variant | 2/10 | 1 | NM_020347.4 | P1 | |
ENST00000699185.1 | n.3796+10591G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250732Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135574
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461274Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726966
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 17 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Dec 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at