chr8-131946605-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015137.6(EFR3A):c.338C>A(p.Pro113Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,603,254 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P113T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015137.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3A | NM_015137.6 | c.338C>A | p.Pro113Gln | missense_variant | 4/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.338C>A | p.Pro113Gln | missense_variant | 4/23 | 1 | NM_015137.6 | P3 | |
EFR3A | ENST00000519656.1 | c.230C>A | p.Pro77Gln | missense_variant | 4/23 | 1 | A1 | ||
EFR3A | ENST00000637848.1 | c.419C>A | p.Pro140Gln | missense_variant | 4/23 | 5 | |||
EFR3A | ENST00000522709.5 | c.230C>A | p.Pro77Gln | missense_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128604
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451192Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 721382
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.338C>A (p.P113Q) alteration is located in exon 4 (coding exon 4) of the EFR3A gene. This alteration results from a C to A substitution at nucleotide position 338, causing the proline (P) at amino acid position 113 to be replaced by a glutamine (Q). 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