NM_001079808.6:c.1057C>G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001079808.6(PGA4):c.1057C>G(p.Leu353Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001079808.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGA4 | NM_001079808.6 | c.1057C>G | p.Leu353Val | missense_variant | Exon 9 of 9 | ENST00000378149.9 | NP_001073276.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 117AN: 31714Hom.: 0 Cov.: 5 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00382 AC: 1288AN: 337266Hom.: 16 Cov.: 0 AF XY: 0.00371 AC XY: 657AN XY: 176980
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00369 AC: 117AN: 31750Hom.: 0 Cov.: 5 AF XY: 0.00393 AC XY: 57AN XY: 14500
ClinVar
Submissions by phenotype
not specified Benign:1
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