NM_031308.4:c.7091G>A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_031308.4(EPPK1):c.7091G>A(p.Arg2364Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_031308.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPPK1 | ENST00000615648.2 | c.7091G>A | p.Arg2364Gln | missense_variant | Exon 2 of 2 | 5 | NM_031308.4 | ENSP00000484472.1 | ||
EPPK1 | ENST00000568225.2 | c.7016G>A | p.Arg2339Gln | missense_variant | Exon 1 of 1 | 6 | ENSP00000456124.2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 11AN: 2526Hom.: 0 Cov.: 2 FAILED QC
GnomAD3 exomes AF: 0.0104 AC: 2054AN: 198012Hom.: 0 AF XY: 0.00924 AC XY: 1002AN XY: 108466
GnomAD4 exome AF: 0.00206 AC: 828AN: 401314Hom.: 9 Cov.: 0 AF XY: 0.00192 AC XY: 406AN XY: 211136
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00431 AC: 11AN: 2550Hom.: 0 Cov.: 2 AF XY: 0.00508 AC XY: 6AN XY: 1182
ClinVar
Submissions by phenotype
EPPK1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at