1-23091432-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000302291.9(LUZP1):c.2830G>A(p.Val944Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,128 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 Likely benign (★).
Frequency
Consequence
ENST00000302291.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LUZP1 | NM_001142546.4 | c.2830G>A | p.Val944Met | missense_variant | 4/5 | NP_001136018.1 | ||
LUZP1 | NM_001395461.1 | c.2830G>A | p.Val944Met | missense_variant | 3/4 | NP_001382390.1 | ||
LUZP1 | NM_001395462.2 | c.2830G>A | p.Val944Met | missense_variant | 3/4 | NP_001382391.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LUZP1 | ENST00000302291.9 | c.2830G>A | p.Val944Met | missense_variant | 3/4 | 5 | ENSP00000303758.4 | |||
LUZP1 | ENST00000314174.5 | c.2830G>A | p.Val944Met | missense_variant | 2/3 | 1 | ENSP00000313705.5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251406Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135878
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727246
GnomAD4 genome AF: 0.000105 AC: 16AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74438
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at