8-131940525-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015137.6(EFR3A):c.37C>T(p.Arg13Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,605,386 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. R13H) 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.37C>T | p.Arg13Cys | missense_variant | 2/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.37C>T | p.Arg13Cys | missense_variant | 2/23 | 1 | NM_015137.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000133 AC: 2AN: 150452Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240846Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130498
GnomAD4 exome AF: 0.0000289 AC: 42AN: 1454934Hom.: 0 Cov.: 33 AF XY: 0.0000263 AC XY: 19AN XY: 723312
GnomAD4 genome ? AF: 0.0000133 AC: 2AN: 150452Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 73258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.37C>T (p.R13C) alteration is located in exon 2 (coding exon 2) of the EFR3A gene. This alteration results from a C to T substitution at nucleotide position 37, causing the arginine (R) at amino acid position 13 to be replaced by a cysteine (C). 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