8-131940526-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015137.6(EFR3A):c.38G>A(p.Arg13His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000873 in 1,603,748 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. R13C) 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.38G>A | p.Arg13His | missense_variant | 2/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.38G>A | p.Arg13His | missense_variant | 2/23 | 1 | NM_015137.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000673 AC: 1AN: 148646Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000828 AC: 2AN: 241516Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130878
GnomAD4 exome AF: 0.00000893 AC: 13AN: 1455102Hom.: 0 Cov.: 33 AF XY: 0.0000111 AC XY: 8AN XY: 723456
GnomAD4 genome ? AF: 0.00000673 AC: 1AN: 148646Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72158
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.38G>A (p.R13H) alteration is located in exon 2 (coding exon 2) of the EFR3A gene. This alteration results from a G to A substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 to be replaced by a histidine (H). 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