1-23091246-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033631.5(LUZP1):c.3016C>T(p.Arg1006Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,613,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033631.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LUZP1 | NM_001142546.4 | c.3016C>T | p.Arg1006Trp | missense_variant | 4/5 | NP_001136018.1 | ||
LUZP1 | NM_001395461.1 | c.3016C>T | p.Arg1006Trp | missense_variant | 3/4 | NP_001382390.1 | ||
LUZP1 | NM_001395462.2 | c.3016C>T | p.Arg1006Trp | missense_variant | 3/4 | NP_001382391.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 250432Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135320
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461590Hom.: 0 Cov.: 30 AF XY: 0.0000908 AC XY: 66AN XY: 727078
GnomAD4 genome AF: 0.000131 AC: 20AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.3016C>T (p.R1006W) alteration is located in exon 4 (coding exon 1) of the LUZP1 gene. This alteration results from a C to T substitution at nucleotide position 3016, causing the arginine (R) at amino acid position 1006 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at