chr1-18636322-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135254.2(PAX7):c.537C>A(p.Asp179Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001135254.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PAX7 | NM_001135254.2 | c.537C>A | p.Asp179Glu | missense_variant | 4/9 | ENST00000420770.7 | |
PAX7 | NM_002584.3 | c.537C>A | p.Asp179Glu | missense_variant | 4/8 | ||
PAX7 | NM_013945.3 | c.531C>A | p.Asp177Glu | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX7 | ENST00000420770.7 | c.537C>A | p.Asp179Glu | missense_variant | 4/9 | 1 | NM_001135254.2 | P1 | |
PAX7 | ENST00000375375.7 | c.537C>A | p.Asp179Glu | missense_variant | 4/8 | 1 | |||
PAX7 | ENST00000400661.3 | c.531C>A | p.Asp177Glu | missense_variant | 4/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249040Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134830
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727214
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.537C>A (p.D179E) alteration is located in exon 4 (coding exon 4) of the PAX7 gene. This alteration results from a C to A substitution at nucleotide position 537, causing the aspartic acid (D) at amino acid position 179 to be replaced by a glutamic acid (E). 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