chr12-112022224-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006817.4(ERP29):c.358C>T(p.Leu120Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,108 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006817.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERP29 | NM_006817.4 | c.358C>T | p.Leu120Phe | missense_variant | Exon 3 of 3 | ENST00000261735.4 | NP_006808.1 | |
ERP29 | NM_001034025.2 | c.*57C>T | 3_prime_UTR_variant | Exon 2 of 2 | NP_001029197.1 | |||
LOC124903021 | XR_007063464.1 | n.-74G>A | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERP29 | ENST00000261735.4 | c.358C>T | p.Leu120Phe | missense_variant | Exon 3 of 3 | 1 | NM_006817.4 | ENSP00000261735.3 | ||
ERP29 | ENST00000546477.1 | c.55C>T | p.Leu19Phe | missense_variant | Exon 3 of 3 | 3 | ENSP00000449018.1 | |||
ERP29 | ENST00000455836.1 | c.*57C>T | 3_prime_UTR_variant | Exon 2 of 2 | 2 | ENSP00000412083.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152238Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251230Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135802
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727204
GnomAD4 genome AF: 0.000177 AC: 27AN: 152356Hom.: 1 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.358C>T (p.L120F) alteration is located in exon 3 (coding exon 3) of the ERP29 gene. This alteration results from a C to T substitution at nucleotide position 358, causing the leucine (L) at amino acid position 120 to be replaced by a phenylalanine (F). 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